explore_dataVariants

today <- Sys.Date() # today's date

Mise à jour du 2021-03-10.
Source des données : https://www.data.gouv.fr/fr/datasets/donnees-de-laboratoires-pour-le-depistage-indicateurs-sur-les-variants/

Légende

library("RColorBrewer")
brw <- brewer.pal(12, "Set3")
brw[2] <- brw[12] # Darker yellow
brw[10] <- brw[11] # Lighter shade
colsAge <- c("#000000FF", brw[1:10])
names(colsAge) <- c("0", "9", "19", "29", "39", "49", "59", "69", "79", "89", "90")
pchAge <- c(16, 0:9)
names(pchAge) <- names(colsAge)
cexAge <- c(1.2, rep(1, 10))
names(cexAge) <- names(colsAge)

ages <- c("tous", "0-9", "10-19", "20-29", "30-39", "40-49", "50-59", "60-69", "70-79", "80-89", "90+")

par(mfrow = c(1, 1))
plot(0:1, 0:1, type = "n", axes = FALSE, xlab = "", ylab = "")
legend(x = 0.5, y = 1, legend = ages, pch = pchAge, col = colsAge)

Données France

Load data

# Données France
URL <- "https://www.data.gouv.fr/fr/datasets/r/c43d7f3f-c9f5-436b-9b26-728f80e0fd52"
dataFile <- paste0("data/France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.France <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)

# Format date
dat.France$date1 <- as.Date(substring(dat.France$semaine, 1, 10))
dat.France$date2 <- as.Date(substring(dat.France$semaine, 12, 21))

# Rewrite time as days since beginning of the data
dat.France$time <- dat.France$date2 - min(dat.France$date2)

# Compute data on total tests
dat.France$Nb_tests_POS <- dat.France$Nb_tests_PCR_TA_crible / (dat.France$Prc_tests_PCR_TA_crible / 100)

# Dictionnary to reformat age class
dic.age <- (0:9)*10 + 4.5 # Median of age classes
names(dic.age) <- as.character(c(0 + (0:8)*10 + 9, 90))

Compare the data to another source – number of positive tests

# Compare to another source
URL <- "https://www.data.gouv.fr/fr/datasets/r/dd0de5d9-b5a5-4503-930a-7b08dc0adc7c"
dataFile <- paste0("data/tests-France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.tests <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)

URL <- "https://www.data.gouv.fr/fr/datasets/r/c1167c4e-8c89-40f2-adb3-1954f8fedfa7"
dataFile <- paste0("data/tests7j-France_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.tests7j <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)
dat.tests7j$date1 <- as.Date(substring(dat.tests7j$semaine_glissante, 1, 10))
dat.tests7j$date2 <- as.Date(substring(dat.tests7j$semaine_glissante, 12, 21))

# P nombre de tests positifs
# T nombre de tests total

dat.tests$date <- as.Date(dat.tests$jour)
dateRange <- range(c(range(dat.France$date1), range(dat.France$date2)))

subdat.tests <- dat.tests[dat.tests$date >= dateRange[1] & dat.tests$date <= dateRange[2],]

# Function to compute a sliding window 
sliding.window <- function(v, winwdt = 7, pos = 4, na.rm = TRUE){
  # v vector to be averaged/summed
  # winwdt width of the window 
  # pos position of the focal day in the window
  # FUN function to apply
  n <- length(v)
  # Initialize output vector
  out <- 0 * v + (-1)
  out[1:(pos-1)] <- NA
  out[(n + 1 - winwdt + pos) : n] <- NA
  
  for(i in pos : (n - winwdt + pos)){
    out[i] <- mean(v[(i - pos + 1):(i + winwdt - pos)], na.rm = na.rm)
  }
  return(out[1:n])
}

subdat.tests.0 <- subdat.tests[subdat.tests$cl_age90 == 0, ]
dat.France.0 <- dat.France[dat.France$cl_age90 == 0, ]

subdat.tests.0$P.7.1 <- 7 * sliding.window(subdat.tests.0$P, pos = 1)
subdat.tests.0$P.7.4 <- 7 * sliding.window(subdat.tests.0$P, pos = 4)
subdat.tests.0$P.7.7 <- 7 * sliding.window(subdat.tests.0$P, pos = 7)
subdat.tests.0$P.8.8 <- 8 * sliding.window(subdat.tests.0$P, pos = 8, winwdt = 8)

plot(dat.France.0$date2, dat.France.0$Nb_tests, ylim = c(1*10^5, 2*10^5), pch = 16, 
     xlab = "date", ylab = "nombre de tests")
points(subdat.tests.0$date, subdat.tests.0$P.7.1, ylim = c(0, 5*10^5), col = "red")
points(subdat.tests.0$date, subdat.tests.0$P.7.4, ylim = c(0, 5*10^5), col = "green")
points(subdat.tests.0$date, subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "blue")
points(subdat.tests.0$date, subdat.tests.0$P.8.8, ylim = c(0, 5*10^5), col = "purple")
points(dat.tests7j$date2, dat.tests7j$P, pch = 2)
legend(x = as.Date("2021-02-18"), y = 200000, col = c("black", "red", "green", "blue", "purple", "black"), legend = c("sidep tests", "w7, c1", "w7, c4", "w7, c7", "w8, c8", "sidep 7j-fin"), pch = c(16, rep(1, 4), 2))

Legend notation:
w: width of the window, c: position of the index day.
So the sliding window is on the 7 last days.
The difference (about 15% more positives in the variants dataset) may be due to the variant data being in terms of tests, and the other in terms of people, with duplicates removed.

#plot(dat.France.0$date2, dat.France.0$Nb_tests, ylim = c(1*10^5, 2*10^5), pch = 16, 
#     xlab = "date", ylab = "comparaison nombre de tests")
#points(subdat.tests.0$date, subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "blue")
#points(subdat.tests.0$date, 1.17*subdat.tests.0$P.7.7, ylim = c(0, 5*10^5), col = "orange")

Format the data further (age class data)

# Data per age class
dat.France.ages <- dat.France[dat.France$cl_age90 != 0,]

# Add new age class code -- median of the age class
dat.France.ages$ageClass <- dic.age[as.character(dat.France.ages$cl_age90)]

# Standardize age class values
dat.France.ages$stdage <- (dat.France.ages$ageClass - mean(dat.France.ages$ageClass))/dat.France.ages$ageClass

V1

Plot

# All ages, time
par(las = 1)
plot(dat.France$date2, dat.France$Prc_susp_501Y_V1, ylim = c(0, 100), 
     col = colsAge[as.character(dat.France$cl_age90)], 
     pch = pchAge[as.character(dat.France$cl_age90)], 
     cex = cexAge[as.character(dat.France$cl_age90)], 
     xlab = "date", ylab = "Proportion V1", axes = FALSE)
axis(1, pos = 0, at = as.Date(unique(dat.France$date2)), labels = format(unique(dat.France$date2), format = "%b %d"))
axis(2)

# Plot dp/(p(1-p)) for each age class
ageClasses <- sort(unique(dat.France$cl_age90))
nAge <- length(ageClasses)

for(iage in unique(dat.France$cl_age90)){
  sub <- dat.France[dat.France$cl_age90 == iage, ]
  V1 <- sub$Prc_susp_501Y_V1/100
  t <- sub$date2
  s <- diff(V1) / (V1[-length(V1)]*(1-V1[-length(V1)]))
  plot(t[-length(V1)], s, ylim = c(-0.1, 0.1),  main = iage)
  print(c(iage, mean(s)))
}

Test

Binomial model

# Create new colums with information on number of specific PCR tests
# PCR with V1 result
dat.France.ages$V1 <- dat.France.ages$Nb_susp_501Y_V1
# All other PCRs (considering NAs are non-V1)
dat.France.ages$notV1 <- dat.France.ages$Nb_tests_PCR_TA_crible - dat.France.ages$Nb_susp_501Y_V1
# All other PCRs with a result (removing NAs)
dat.France.ages$notV1.narm <- dat.France.ages$Nb_susp_501Y_V2_3 + dat.France.ages$Nb_susp_ABS

# Check that columns correctly sum
all(dat.France.ages$Nb_susp_501Y_V2_3 + dat.France.ages$Nb_susp_ABS + dat.France.ages$Nb_susp_501Y_V1 + dat.France.ages$Nb_susp_IND - dat.France.ages$Nb_tests_PCR_TA_crible == 0)

## [1] TRUE

GLM, assume that all indeterminate PCRs are non-V1

1. Age as factor, compare models without and with interaction between age and time

# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0 <- glm(cbind(V1, notV1) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass), family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##    Min      1Q  Median      3Q     Max  
## -3.814  -1.069   0.078   1.077   6.067  
## 
## Coefficients:
##                            Estimate Std. Error z value Pr(>|z|)    
## (Intercept)                0.049088   0.014536   3.377 0.000733 ***
## time                       0.042181   0.001451  29.069  < 2e-16 ***
## factor(ageClass)14.5      -0.125984   0.016757  -7.518 5.56e-14 ***
## factor(ageClass)24.5      -0.192926   0.016513 -11.684  < 2e-16 ***
## factor(ageClass)34.5      -0.119481   0.016474  -7.253 4.09e-13 ***
## factor(ageClass)44.5      -0.117069   0.016449  -7.117 1.10e-12 ***
## factor(ageClass)54.5      -0.231182   0.016612 -13.917  < 2e-16 ***
## factor(ageClass)64.5      -0.353565   0.017387 -20.335  < 2e-16 ***
## factor(ageClass)74.5      -0.638756   0.018946 -33.714  < 2e-16 ***
## factor(ageClass)84.5      -0.908481   0.020351 -44.641  < 2e-16 ***
## factor(ageClass)94.5      -1.050222   0.024957 -42.081  < 2e-16 ***
## time:factor(ageClass)14.5  0.007233   0.001674   4.321 1.55e-05 ***
## time:factor(ageClass)24.5  0.011140   0.001649   6.754 1.44e-11 ***
## time:factor(ageClass)34.5  0.006262   0.001649   3.797 0.000146 ***
## time:factor(ageClass)44.5  0.007053   0.001649   4.279 1.88e-05 ***
## time:factor(ageClass)54.5  0.009721   0.001664   5.843 5.11e-09 ***
## time:factor(ageClass)64.5  0.009909   0.001736   5.708 1.14e-08 ***
## time:factor(ageClass)74.5  0.024368   0.001893  12.869  < 2e-16 ***
## time:factor(ageClass)84.5  0.023884   0.002059  11.601  < 2e-16 ***
## time:factor(ageClass)94.5  0.019724   0.002594   7.603 2.90e-14 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 47557.1  on 179  degrees of freedom
## Residual deviance:   531.3  on 160  degrees of freedom
## AIC: 2267
## 
## Number of Fisher Scoring iterations: 3

# Without interaction
mdl1 <- glm(cbind(V1, notV1) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time + factor(ageClass), family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.3209  -1.2307   0.2074   1.1558   7.8383  
## 
## Coefficients:
##                        Estimate Std. Error z value Pr(>|z|)    
## (Intercept)          -0.0371071  0.0078627  -4.719 2.37e-06 ***
## time                  0.0522049  0.0003046 171.379  < 2e-16 ***
## factor(ageClass)14.5 -0.0638032  0.0085359  -7.475 7.74e-14 ***
## factor(ageClass)24.5 -0.0970938  0.0084020 -11.556  < 2e-16 ***
## factor(ageClass)34.5 -0.0652612  0.0084078  -7.762 8.36e-15 ***
## factor(ageClass)44.5 -0.0559737  0.0083973  -6.666 2.63e-11 ***
## factor(ageClass)54.5 -0.1475708  0.0084601 -17.443  < 2e-16 ***
## factor(ageClass)64.5 -0.2683637  0.0088228 -30.417  < 2e-16 ***
## factor(ageClass)74.5 -0.4283992  0.0095582 -44.820  < 2e-16 ***
## factor(ageClass)84.5 -0.7066547  0.0103922 -67.998  < 2e-16 ***
## factor(ageClass)94.5 -0.8866586  0.0130249 -68.074  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 47557.14  on 179  degrees of freedom
## Residual deviance:   880.71  on 169  degrees of freedom
## AIC: 2598.4
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl1, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time + factor(ageClass)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       169     880.71                          
## 2       160     531.30  9   349.41 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Age as quantitative

# Test date effect
mdl2 <- glm(cbind(V1, notV1) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * ageClass, family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -12.544   -6.159   -1.694    3.303   12.919  
## 
## Coefficients:
##                 Estimate Std. Error z value Pr(>|z|)    
## (Intercept)    1.712e-01  6.496e-03   26.35   <2e-16 ***
## time           4.309e-02  6.566e-04   65.64   <2e-16 ***
## ageClass      -8.865e-03  1.344e-04  -65.98   <2e-16 ***
## time:ageClass  2.204e-04  1.368e-05   16.11   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 47557.1  on 179  degrees of freedom
## Residual deviance:  5714.8  on 176  degrees of freedom
## AIC: 7418.5
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl2, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time * ageClass
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       176     5714.8                          
## 2       160      531.3 16   5183.5 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

GLM, ignore indeterminate PCRs

1. Age as factor, compare models without and with interaction between age and time

# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0.narm <- glm(cbind(V1, notV1.narm) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0.narm)

## 
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time * factor(ageClass), 
##     family = "binomial", data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -4.0694  -1.0888   0.0445   1.1808   6.5207  
## 
## Coefficients:
##                            Estimate Std. Error z value Pr(>|z|)    
## (Intercept)                0.272629   0.015719  17.344  < 2e-16 ***
## time                       0.049916   0.001598  31.232  < 2e-16 ***
## factor(ageClass)14.5      -0.189098   0.018013 -10.498  < 2e-16 ***
## factor(ageClass)24.5      -0.249451   0.017769 -14.039  < 2e-16 ***
## factor(ageClass)34.5      -0.172360   0.017729  -9.722  < 2e-16 ***
## factor(ageClass)44.5      -0.175171   0.017692  -9.901  < 2e-16 ***
## factor(ageClass)54.5      -0.292472   0.017849 -16.386  < 2e-16 ***
## factor(ageClass)64.5      -0.417649   0.018624 -22.425  < 2e-16 ***
## factor(ageClass)74.5      -0.697555   0.020196 -34.539  < 2e-16 ***
## factor(ageClass)84.5      -0.973347   0.021578 -45.108  < 2e-16 ***
## factor(ageClass)94.5      -1.129383   0.026191 -43.121  < 2e-16 ***
## time:factor(ageClass)14.5  0.005881   0.001831   3.211 0.001321 ** 
## time:factor(ageClass)24.5  0.011331   0.001807   6.269 3.63e-10 ***
## time:factor(ageClass)34.5  0.005380   0.001806   2.979 0.002896 ** 
## time:factor(ageClass)44.5  0.005041   0.001804   2.794 0.005204 ** 
## time:factor(ageClass)54.5  0.006868   0.001818   3.778 0.000158 ***
## time:factor(ageClass)64.5  0.006843   0.001890   3.620 0.000295 ***
## time:factor(ageClass)74.5  0.022417   0.002053  10.921  < 2e-16 ***
## time:factor(ageClass)84.5  0.022285   0.002218  10.046  < 2e-16 ***
## time:factor(ageClass)94.5  0.018750   0.002762   6.787 1.14e-11 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 50201.02  on 179  degrees of freedom
## Residual deviance:   615.12  on 160  degrees of freedom
## AIC: 2327.9
## 
## Number of Fisher Scoring iterations: 3

# Without interaction
mdl1.narm <- glm(cbind(V1, notV1.narm) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1.narm)

## 
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time + factor(ageClass), 
##     family = "binomial", data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.3553  -1.3565   0.1452   1.2478   7.6394  
## 
## Coefficients:
##                        Estimate Std. Error z value Pr(>|z|)    
## (Intercept)           0.2007295  0.0085771   23.40   <2e-16 ***
## time                  0.0584876  0.0003257  179.57   <2e-16 ***
## factor(ageClass)14.5 -0.1399048  0.0093042  -15.04   <2e-16 ***
## factor(ageClass)24.5 -0.1542727  0.0091738  -16.82   <2e-16 ***
## factor(ageClass)34.5 -0.1270116  0.0091778  -13.84   <2e-16 ***
## factor(ageClass)44.5 -0.1325456  0.0091581  -14.47   <2e-16 ***
## factor(ageClass)54.5 -0.2348562  0.0092135  -25.49   <2e-16 ***
## factor(ageClass)64.5 -0.3604909  0.0095800  -37.63   <2e-16 ***
## factor(ageClass)74.5 -0.5078669  0.0103394  -49.12   <2e-16 ***
## factor(ageClass)84.5 -0.7889338  0.0111574  -70.71   <2e-16 ***
## factor(ageClass)94.5 -0.9776377  0.0138001  -70.84   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 50201.02  on 179  degrees of freedom
## Residual deviance:   919.41  on 169  degrees of freedom
## AIC: 2614.2
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl1.narm, mdl0.narm, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1.narm) ~ time + factor(ageClass)
## Model 2: cbind(V1, notV1.narm) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       169     919.41                          
## 2       160     615.12  9    304.3 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Age as quantitative

# Test date effect
mdl2.narm <- glm(cbind(V1, notV1.narm) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2.narm)

## 
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ time * ageClass, family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##      Min        1Q    Median        3Q       Max  
## -12.0104   -5.3925   -0.5634    3.0613   12.6203  
## 
## Coefficients:
##                 Estimate Std. Error z value Pr(>|z|)    
## (Intercept)    3.522e-01  6.894e-03   51.09   <2e-16 ***
## time           5.061e-02  7.079e-04   71.50   <2e-16 ***
## ageClass      -9.205e-03  1.419e-04  -64.89   <2e-16 ***
## time:ageClass  1.897e-04  1.466e-05   12.94   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 50201.0  on 179  degrees of freedom
## Residual deviance:  5018.8  on 176  degrees of freedom
## AIC: 6699.6
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl2.narm, mdl0.narm, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1.narm) ~ time * ageClass
## Model 2: cbind(V1, notV1.narm) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       176     5018.8                          
## 2       160      615.1 16   4403.7 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

V2/V3

Plot

# All ages, time
par(las = 1)
plot(dat.France$date2, dat.France$Prc_susp_501Y_V2_3, ylim = c(0, 100), 
     col = colsAge[as.character(dat.France$cl_age90)], 
     pch = pchAge[as.character(dat.France$cl_age90)], 
     cex = cexAge[as.character(dat.France$cl_age90)], 
     xlab = "date", ylab = "Proportion V2/V3", axes = FALSE)
axis(1, pos = 0, at = as.Date(unique(dat.France$date2)), labels = format(unique(dat.France$date2), format = "%b %d"))
axis(2)

Test

Binomial

# Create new colums with information on number of specific PCR tests
# PCR with V2/V3 result
dat.France.ages$V23 <- dat.France.ages$Nb_susp_501Y_V2_3
# All other PCRs (considering NAs are non-V23)
dat.France.ages$notV23 <- dat.France.ages$Nb_tests_PCR_TA_crible - dat.France.ages$Nb_susp_501Y_V2_3
# All other PCRs with a result (removing NAs)
dat.France.ages$notV23.narm <- dat.France.ages$Nb_susp_501Y_V1 + dat.France.ages$Nb_susp_ABS

GLM, assume that all indeterminate PCRs are non-V1

1. Age as factor, compare models without and with interaction between age and time

# GLM
# Assuming that all IND (indetermine) are non-V23
mdl0 <- glm(cbind(V23, notV23) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0)

## 
## Call:
## glm(formula = cbind(V23, notV23) ~ time * factor(ageClass), family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -3.2343  -0.8336  -0.0472   0.7092   3.0681  
## 
## Coefficients:
##                             Estimate Std. Error z value Pr(>|z|)    
## (Intercept)               -3.101e+00  3.501e-02 -88.564  < 2e-16 ***
## time                       6.063e-03  3.386e-03   1.790  0.07338 .  
## factor(ageClass)14.5       2.491e-01  3.946e-02   6.312 2.76e-10 ***
## factor(ageClass)24.5       2.582e-01  3.897e-02   6.624 3.49e-11 ***
## factor(ageClass)34.5       3.928e-02  3.937e-02   0.998  0.31835    
## factor(ageClass)44.5       2.848e-02  3.943e-02   0.722  0.47008    
## factor(ageClass)54.5       5.972e-02  3.967e-02   1.505  0.13223    
## factor(ageClass)64.5       2.046e-01  4.082e-02   5.012 5.38e-07 ***
## factor(ageClass)74.5      -2.533e-01  4.720e-02  -5.366 8.06e-08 ***
## factor(ageClass)84.5      -3.326e-01  5.142e-02  -6.468 9.90e-11 ***
## factor(ageClass)94.5      -2.731e-01  6.156e-02  -4.436 9.17e-06 ***
## time:factor(ageClass)14.5 -6.631e-03  3.830e-03  -1.731  0.08339 .  
## time:factor(ageClass)24.5 -9.150e-03  3.785e-03  -2.418  0.01563 *  
## time:factor(ageClass)34.5  1.080e-02  3.802e-03   2.841  0.00449 ** 
## time:factor(ageClass)44.5  5.700e-03  3.819e-03   1.493  0.13552    
## time:factor(ageClass)54.5  6.660e-03  3.841e-03   1.734  0.08293 .  
## time:factor(ageClass)64.5 -8.279e-06  3.960e-03  -0.002  0.99833    
## time:factor(ageClass)74.5  1.245e-02  4.559e-03   2.730  0.00633 ** 
## time:factor(ageClass)84.5  9.013e-03  5.099e-03   1.767  0.07715 .  
## time:factor(ageClass)94.5  1.210e-02  6.311e-03   1.918  0.05517 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1702.41  on 179  degrees of freedom
## Residual deviance:  315.07  on 160  degrees of freedom
## AIC: 1747.5
## 
## Number of Fisher Scoring iterations: 3

# Without interaction
mdl1 <- glm(cbind(V23, notV23) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1)

## 
## Call:
## glm(formula = cbind(V23, notV23) ~ time + factor(ageClass), family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -4.8227  -1.0518   0.1092   0.9814   3.2845  
## 
## Coefficients:
##                        Estimate Std. Error  z value Pr(>|z|)    
## (Intercept)          -3.1198628  0.0183534 -169.988  < 2e-16 ***
## time                  0.0081962  0.0006807   12.040  < 2e-16 ***
## factor(ageClass)14.5  0.1901572  0.0195394    9.732  < 2e-16 ***
## factor(ageClass)24.5  0.1770289  0.0193008    9.172  < 2e-16 ***
## factor(ageClass)34.5  0.1366049  0.0193766    7.050 1.79e-12 ***
## factor(ageClass)44.5  0.0794749  0.0194558    4.085 4.41e-05 ***
## factor(ageClass)54.5  0.1193852  0.0195467    6.108 1.01e-09 ***
## factor(ageClass)64.5  0.2047544  0.0201562   10.158  < 2e-16 ***
## factor(ageClass)74.5 -0.1416976  0.0231138   -6.130 8.76e-10 ***
## factor(ageClass)84.5 -0.2556056  0.0259329   -9.856  < 2e-16 ***
## factor(ageClass)94.5 -0.1746847  0.0319622   -5.465 4.62e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1702.41  on 179  degrees of freedom
## Residual deviance:  438.73  on 169  degrees of freedom
## AIC: 1853.2
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl1, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V23, notV23) ~ time + factor(ageClass)
## Model 2: cbind(V23, notV23) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       169     438.73                          
## 2       160     315.07  9   123.67 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Age as quantitative

# Test date effect
mdl2 <- glm(cbind(V23, notV23) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2)

## 
## Call:
## glm(formula = cbind(V23, notV23) ~ time * ageClass, family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -4.5268  -2.5430  -0.9477   1.3786   5.1717  
## 
## Coefficients:
##                 Estimate Std. Error  z value Pr(>|z|)    
## (Intercept)   -2.810e+00  1.464e-02 -192.018  < 2e-16 ***
## time          -1.128e-03  1.435e-03   -0.786    0.432    
## ageClass      -5.004e-03  3.132e-04  -15.975  < 2e-16 ***
## time:ageClass  2.347e-04  3.085e-05    7.609 2.76e-14 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1702.4  on 179  degrees of freedom
## Residual deviance: 1117.2  on 176  degrees of freedom
## AIC: 2517.6
## 
## Number of Fisher Scoring iterations: 4

## Likelihood ratio test
anova(mdl2, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V23, notV23) ~ time * ageClass
## Model 2: cbind(V23, notV23) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       176    1117.16                          
## 2       160     315.07 16    802.1 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

GLM, ignore indeterminate PCRs

1. Age as factor, compare models without and with interaction between age and time

# GLM
# Assuming that all IND (indetermine) are non-V23
mdl0.narm <- glm(cbind(V23, notV23.narm) ~ time * factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl0.narm)

## 
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time * factor(ageClass), 
##     family = "binomial", data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -3.1803  -0.7890  -0.0710   0.7139   3.0180  
## 
## Coefficients:
##                             Estimate Std. Error z value Pr(>|z|)    
## (Intercept)               -2.9887015  0.0351726 -84.972  < 2e-16 ***
## time                       0.0057683  0.0034042   1.694  0.09018 .  
## factor(ageClass)14.5       0.2261837  0.0396327   5.707 1.15e-08 ***
## factor(ageClass)24.5       0.2427125  0.0391383   6.201 5.60e-10 ***
## factor(ageClass)34.5       0.0200154  0.0395290   0.506  0.61261    
## factor(ageClass)44.5       0.0057322  0.0395889   0.145  0.88487    
## factor(ageClass)54.5       0.0405250  0.0398441   1.017  0.30911    
## factor(ageClass)64.5       0.1897116  0.0409918   4.628 3.69e-06 ***
## factor(ageClass)74.5      -0.2536145  0.0473419  -5.357 8.46e-08 ***
## factor(ageClass)84.5      -0.3257049  0.0515909  -6.313 2.73e-10 ***
## factor(ageClass)94.5      -0.2713405  0.0617731  -4.393 1.12e-05 ***
## time:factor(ageClass)14.5 -0.0065839  0.0038484  -1.711  0.08711 .  
## time:factor(ageClass)24.5 -0.0089406  0.0038028  -2.351  0.01872 *  
## time:factor(ageClass)34.5  0.0110257  0.0038192   2.887  0.00389 ** 
## time:factor(ageClass)44.5  0.0056161  0.0038363   1.464  0.14321    
## time:factor(ageClass)54.5  0.0062869  0.0038597   1.629  0.10334    
## time:factor(ageClass)64.5 -0.0003364  0.0039785  -0.085  0.93262    
## time:factor(ageClass)74.5  0.0119004  0.0045732   2.602  0.00926 ** 
## time:factor(ageClass)84.5  0.0090968  0.0051181   1.777  0.07551 .  
## time:factor(ageClass)94.5  0.0133106  0.0063357   2.101  0.03565 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1555.35  on 179  degrees of freedom
## Residual deviance:  308.18  on 160  degrees of freedom
## AIC: 1739.8
## 
## Number of Fisher Scoring iterations: 3

# Without interaction
mdl1.narm <- glm(cbind(V23, notV23.narm) ~ time + factor(ageClass), data = dat.France.ages, family = "binomial")
summary(mdl1.narm)

## 
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time + factor(ageClass), 
##     family = "binomial", data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -4.7997  -1.0008   0.0805   0.9932   3.2320  
## 
## Coefficients:
##                        Estimate Std. Error  z value Pr(>|z|)    
## (Intercept)          -3.0077065  0.0184010 -163.454  < 2e-16 ***
## time                  0.0078766  0.0006825   11.541  < 2e-16 ***
## factor(ageClass)14.5  0.1676880  0.0195899    8.560  < 2e-16 ***
## factor(ageClass)24.5  0.1634677  0.0193516    8.447  < 2e-16 ***
## factor(ageClass)34.5  0.1193159  0.0194269    6.142 8.16e-10 ***
## factor(ageClass)44.5  0.0559718  0.0195050    2.870  0.00411 ** 
## factor(ageClass)54.5  0.0968684  0.0195965    4.943 7.69e-07 ***
## factor(ageClass)64.5  0.1869081  0.0202091    9.249  < 2e-16 ***
## factor(ageClass)74.5 -0.1468689  0.0231697   -6.339 2.32e-10 ***
## factor(ageClass)84.5 -0.2480370  0.0259946   -9.542  < 2e-16 ***
## factor(ageClass)94.5 -0.1635410  0.0320422   -5.104 3.33e-07 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1555.35  on 179  degrees of freedom
## Residual deviance:  429.68  on 169  degrees of freedom
## AIC: 1843.3
## 
## Number of Fisher Scoring iterations: 3

## Likelihood ratio test
anova(mdl1.narm, mdl0.narm, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V23, notV23.narm) ~ time + factor(ageClass)
## Model 2: cbind(V23, notV23.narm) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       169     429.68                          
## 2       160     308.18  9    121.5 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Age as quantitative

# Test date effect
mdl2.narm <- glm(cbind(V23, notV23.narm) ~ time * ageClass, data = dat.France.ages, family = "binomial")
summary(mdl2.narm)

## 
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ time * ageClass, family = "binomial", 
##     data = dat.France.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -4.1401  -2.4294  -0.7728   1.2912   5.1410  
## 
## Coefficients:
##                 Estimate Std. Error  z value Pr(>|z|)    
## (Intercept)   -2.721e+00  1.472e-02 -184.888  < 2e-16 ***
## time          -1.211e-03  1.444e-03   -0.838    0.402    
## ageClass      -4.826e-03  3.152e-04  -15.311  < 2e-16 ***
## time:ageClass  2.284e-04  3.105e-05    7.354 1.93e-13 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 1555.4  on 179  degrees of freedom
## Residual deviance: 1021.6  on 176  degrees of freedom
## AIC: 2421.2
## 
## Number of Fisher Scoring iterations: 4

## Likelihood ratio test
anova(mdl2.narm, mdl0.narm, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V23, notV23.narm) ~ time * ageClass
## Model 2: cbind(V23, notV23.narm) ~ time * factor(ageClass)
##   Resid. Df Resid. Dev Df Deviance  Pr(>Chi)    
## 1       176    1021.62                          
## 2       160     308.18 16   713.44 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Multinomial

Prepare plots for distribution of variants

par(mfrow = c(1, 1))

getVec <- function(dataset, prop = TRUE){
  if(prop){
    nn <- 1
  }else{
    nn <- dataset$Nb_tests_POS / 7 # Divide by 7 to have average over the week instead of sum
  }
  x <- dataset$date2
  c1 <- dataset$Prc_susp_501Y_V1/100 * nn
  c23 <- c1 + dataset$Prc_susp_501Y_V2_3/100 * nn
  cABS <- c23 + dataset$Prc_susp_ABS/100 * nn
  cIND <- cABS + dataset$Prc_susp_IND/100 * nn
  list(x = x, c1 = c1, c23 = c23, cABS = cABS, cIND = cIND)
}

colV <- c(brewer.pal(3, "Set2"), gray(0.5))

plotDist <- function(x, c1, c23, cABS, cIND){
  if(max(cIND, na.rm = TRUE) == 1 | max(cIND, na.rm = TRUE) == 100 | max(c1, na.rm = TRUE) > 100){
    yl <- "Proportions variants"
  }else{
    yl <- "Number cases"
  }
  plot(x, c1, ylim = c(0, max(cIND)), type = "l", 
       xlab = "date", ylab = yl, axes = FALSE)
  axis(1, pos = 0, labels = format(x, "%b-%d"), at = x)
  axis(2, pos = x[1])
  polygon(c(x, rev(x)), c(rep(0, length(x)), rev(c1)), col = colV[1], border = NULL)
  polygon(c(x, rev(x)), c(c1, rev(c23)), col = colV[2], border = NULL)
  polygon(c(x, rev(x)), c(c23, rev(cABS)), col = colV[3], border = NULL)
  polygon(c(x, rev(x)), c(cABS, rev(cIND)), col = colV[4], border = NULL)
  
  nend <- length(x)-1
  text(x = rep(x[nend], 4), y = c(c1[nend]/2, c1[nend] + (c23[nend] - c1[nend])/2, c23[nend] + (cABS[nend] - c23[nend])/2, cABS[nend] + (cIND[nend] - cABS[nend])/2), labels = c("V1", "V2/V3", "WT", "indet."), col = "white", adj = 1)
}

Frequencies

cc <- getVec(dat.France.0, prop = TRUE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)

Densities

cc <- getVec(dat.France.0, prop = FALSE)
plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)

mat <- as.matrix(data.frame(WT = dat.France.ages$Nb_susp_ABS, 
                            V1 = dat.France.ages$Nb_susp_501Y_V1, 
                            V2 = dat.France.ages$Nb_susp_501Y_V2_3, 
                            INDET = dat.France.ages$Nb_susp_IND))

library(nnet)

## Null model
m0 <- multinom(mat ~ 1)

## # weights:  8 (3 variable)
## initial  value 2460671.104693 
## final  value 1855506.003454 
## converged

summary(m0)

## Call:
## multinom(formula = mat ~ 1)
## 
## Coefficients:
##       (Intercept)
## V1      0.6119623
## V2     -1.8046807
## INDET  -1.2781219
## 
## Std. Errors:
##       (Intercept)
## V1    0.001690021
## V2    0.003620477
## INDET 0.002915485
## 
## Residual Deviance: 3711012 
## AIC: 3711018

## Compute by hand to check result
log(colSums(mat)[2]/colSums(mat)[1])

##        V1 
## 0.6120011

log(colSums(mat)[3]/colSums(mat)[1])

##        V2 
## -1.804692

log(colSums(mat)[4]/colSums(mat)[1])

##     INDET 
## -1.277982

## Time effect
m1 <- multinom(mat ~ time, data=dat.France.ages)

## # weights:  12 (6 variable)
## initial  value 2460671.104693 
## iter  10 value 1835784.719195
## final  value 1835774.796613 
## converged

summary(m1)

## Call:
## multinom(formula = mat ~ time, data = dat.France.ages)
## 
## Coefficients:
##       (Intercept)       time
## V1     0.04833576 0.06676898
## V2    -2.23282492 0.05187632
## INDET -1.59432367 0.03910026
## 
## Std. Errors:
##       (Intercept)         time
## V1    0.003277047 0.0003410188
## V2    0.007259751 0.0007204104
## INDET 0.005663837 0.0005796311
## 
## Residual Deviance: 3671550 
## AIC: 3671562

## Likelihood ratio test
anova(m0, m1, test="Chisq")

##   Model Resid. df Resid. Dev   Test    Df LR stat. Pr(Chi)
## 1     1       537    3711012           NA       NA      NA
## 2  time       534    3671550 1 vs 2     3 39462.41       0

## Age effect
m2 <- multinom(mat ~ time + stdage, data=dat.France.ages)

## # weights:  16 (9 variable)
## initial  value 2460671.104693 
## iter  10 value 1853648.120734
## final  value 1834148.253751 
## converged

summary(m2)

## Call:
## multinom(formula = mat ~ time + stdage, data = dat.France.ages)
## 
## Coefficients:
##        (Intercept)       time      stdage
## V1     0.008541788 0.06662480 -0.04747537
## V2    -2.261699066 0.05177393 -0.03549250
## INDET -1.629594672 0.03897770 -0.04254707
## 
## Std. Errors:
##       (Intercept)         time       stdage
## V1    0.003355564 0.0003413456 0.0008613089
## V2    0.007412590 0.0007205136 0.0017311923
## INDET 0.005793389 0.0005797807 0.0013831851
## 
## Residual Deviance: 3668297 
## AIC: 3668315

## Likelihood ratio test
anova(m1, m2, test="Chisq")

##           Model Resid. df Resid. Dev   Test    Df LR stat. Pr(Chi)
## 1          time       534    3671550           NA       NA      NA
## 2 time + stdage       531    3668297 1 vs 2     3 3253.086       0

## Age effect
m3 <- multinom(mat ~ time * stdage, data=dat.France.ages)

## # weights:  20 (12 variable)
## initial  value 2460671.104693 
## iter  10 value 1924569.724771
## iter  20 value 1834100.956963
## final  value 1834100.925004 
## converged

summary(m3)

## Call:
## multinom(formula = mat ~ time * stdage, data = dat.France.ages)
## 
## Coefficients:
##        (Intercept)       time      stdage   time:stdage
## V1    -0.001225914 0.06782063 -0.05896115  1.402145e-03
## V2    -2.273416450 0.05321451 -0.04936935  1.694381e-03
## INDET -1.626780979 0.03873798 -0.04086087 -8.504092e-05
## 
## Std. Errors:
##       (Intercept)         time      stdage  time:stdage
## V1    0.003550246 0.0003703003 0.001631136 0.0001694933
## V2    0.007881503 0.0007836125 0.003401622 0.0003402115
## INDET 0.006143479 0.0006308728 0.002696711 0.0002720972
## 
## Residual Deviance: 3668202 
## AIC: 3668226

## Likelihood ratio test
anova(m2, m3, test="Chisq")

##           Model Resid. df Resid. Dev   Test    Df LR stat. Pr(Chi)
## 1 time + stdage       531    3668297           NA       NA      NA
## 2 time * stdage       528    3668202 1 vs 2     3 94.65749       0

Pb in the data is the change in the age structure of positive individuals; to really test the effet, we would need information on the negative tests as well, and the age distribution in these negative tests.

tapply(dat.France.ages$Nb_tests_PCR_TA_crible, list(dat.France.ages$cl_age90, dat.France.ages$time), sum)

##        0     1     2     3     4     5     6     7     8     9    10    11
## 9   3564  3813  3912  3941  4008  4095  4234  4328  4475  4495  4482  4518
## 19 10508 11441 11845 11909 12446 12826 13136 13452 13654 13682 13722 13845
## 29 11675 12907 13335 13458 14294 14853 15206 15457 15499 15638 15666 15751
## 39 12290 13317 13784 13833 14486 14998 15237 15496 15580 15556 15616 15690
## 49 12409 13542 14010 14130 14825 15339 15693 15763 15843 15952 15958 15935
## 59 11174 12289 12777 12874 13663 14167 14501 14816 14911 14916 14913 14791
## 69  8010  8781  9038  9106  9586  9918 10244 10491 10533 10660 10655 10723
## 79  5152  5589  5813  5887  6063  6374  6543  6614  6675  6680  6649  6676
## 89  4291  4601  4706  4773  4788  4775  4756  4644  4596  4562  4545  4373
## 90  2385  2472  2520  2551  2503  2470  2358  2281  2203  2182  2170  1991
##       12    13    14    15    16    17
## 9   4563  4546  4610  4571  4539  4544
## 19 13869 13936 13848 13676 13613 13580
## 29 15881 15885 15857 15579 15427 15334
## 39 15562 15575 15324 15005 14952 14868
## 49 15760 15594 15464 14928 14723 14634
## 59 14654 14450 14122 13734 13542 13487
## 69 10707 10529 10348 10089  9902  9810
## 79  6537  6410  6254  6073  5991  5940
## 89  4264  4079  3939  3750  3650  3591
## 90  1863  1751  1634  1553  1521  1478

Données régions

Load data

URL <- "https://www.data.gouv.fr/fr/datasets/r/73e8851a-d851-43f8-89e4-6178b35b7127"
dataFile <- paste0("data/Regions_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.regions <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)

# Format date
dat.regions$date1 <- as.Date(substring(dat.regions$semaine, 1, 10))
dat.regions$date2 <- as.Date(substring(dat.regions$semaine, 12, 21))

# Rewrite time as days since beginning of the data
dat.regions$time <- dat.regions$date2 - min(dat.regions$date2)

# Compute data on total tests
dat.regions$Nb_tests_POS <- dat.regions$Nb_tests_PCR_TA_crible / (dat.regions$Prc_tests_PCR_TA_crible / 100)

# Codes regions
URL <- "https://www.data.gouv.fr/en/datasets/r/34fc7b52-ef11-4ab0-bc16-e1aae5c942e7"
dataFile <- "data/coderegions.csv"
download.file(URL, dataFile)
codesRegions <- read.csv(dataFile, sep = ",", stringsAsFactors = FALSE)

# Turn into dictionary
regs <- codesRegions$nom_region
names(regs) <- as.character(codesRegions$code_region)

# Add region name
dat.regions$reg_name <- regs[as.character(dat.regions$reg)]
# dat.regions[floor(runif(10)*1000), c("reg", "reg_name")] # check a few names

# What are the other regions??
# aggregate(dat.regions$reg, by = list(dat.regions$reg), FUN = length)

Format data further

dat.regions.ages <- dat.regions[dat.regions$cl_age90 != 0,]

# Add new age class code -- median of the age class
dat.regions.ages$ageClass <- dic.age[as.character(dat.regions.ages$cl_age90)]

# Standardize age class values
dat.regions.ages$stdage <- (dat.regions.ages$ageClass - mean(dat.regions.ages$ageClass))/dat.regions.ages$ageClass

V1

Plot

tmp <- unique(dat.regions$reg) # Region codes
tmp <- tmp[tmp>10 & tmp <= 93] # Choose only metropolitan regions
par(mfrow = c(4, 3))
for(region in tmp){
  subdat <- dat.regions[dat.regions$reg == region, ]
  plot(subdat$date2, subdat$Prc_susp_501Y_V1, ylim = c(0, 100), main = regs[as.character(region)], col = colsAge[as.character(subdat$cl_age90)], pch = pchAge[as.character(subdat$cl_age90)], 
       xlab = "date", ylab = "Proportion V1"
       )
}

Test

# Create new colums with information on number of specific PCR tests
# PCR with V1 result
dat.regions.ages$V1 <- dat.regions.ages$Nb_susp_501Y_V1
# All other PCRs (considering NAs are non-V1)
dat.regions.ages$notV1 <- dat.regions.ages$Nb_tests_PCR_TA_crible - dat.regions.ages$Nb_susp_501Y_V1
# All other PCRs with a result (removing NAs)
dat.regions.ages$notV1.narm <- dat.regions.ages$Nb_susp_501Y_V2_3 + dat.regions.ages$Nb_susp_ABS

# Check that columns currently sum
all(dat.regions.ages$Nb_susp_501Y_V2_3 + dat.regions.ages$Nb_susp_ABS + dat.regions.ages$Nb_susp_501Y_V1 + dat.regions.ages$Nb_susp_IND - dat.regions.ages$Nb_tests_PCR_TA_crible == 0)

## [1] TRUE

dat.regions.ages$reg_name.fac <- as.factor(dat.regions.ages$reg_name)

GLM, assume that all indeterminate PCRs are non-V1

1. Age as factor, compare models without and with interaction between age and time

# GLM
# Assuming that all IND (indetermine) are non-V1
mdl0 <- glm(cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name), data = dat.regions.ages, family = "binomial")

## Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred

summary(mdl0)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name), 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -3.2242  -0.4580   0.0000   0.4603   4.0993  
## 
## Coefficients: (11 not defined because of singularities)
##                                                                        Estimate
## (Intercept)                                                          -1.684e-01
## time                                                                  5.144e-02
## factor(ageClass)14.5                                                 -5.234e-03
## factor(ageClass)24.5                                                 -2.009e-01
## factor(ageClass)34.5                                                 -1.763e-01
## factor(ageClass)44.5                                                 -2.080e-01
## factor(ageClass)54.5                                                 -3.267e-01
## factor(ageClass)64.5                                                 -5.585e-01
## factor(ageClass)74.5                                                 -6.705e-01
## factor(ageClass)84.5                                                 -9.681e-01
## factor(ageClass)94.5                                                 -1.127e+00
## factor(reg_name)Bourgogne-Franche-Comté                              -5.311e-01
## factor(reg_name)Bretagne                                              6.454e-01
## factor(reg_name)Centre-Val de Loire                                  -2.424e-02
## factor(reg_name)Corse                                                 2.778e+00
## factor(reg_name)Grand Est                                            -6.609e-01
## factor(reg_name)Guadeloupe                                           -1.627e+02
## factor(reg_name)Guyane                                               -1.840e+01
## factor(reg_name)Hauts-de-France                                       4.812e-01
## factor(reg_name)Île-de-France                                         5.822e-01
## factor(reg_name)La Réunion                                           -3.214e+00
## factor(reg_name)Martinique                                           -2.733e+00
## factor(reg_name)Mayotte                                               1.986e+01
## factor(reg_name)Normandie                                            -1.129e-01
## factor(reg_name)Nouvelle-Aquitaine                                    2.153e-01
## factor(reg_name)Occitanie                                             2.685e-01
## factor(reg_name)Pays de la Loire                                     -2.237e-01
## factor(reg_name)Provence-Alpes-Côte d'Azur                            4.653e-01
## time:factor(ageClass)14.5                                            -1.328e-02
## time:factor(ageClass)24.5                                             2.605e-03
## time:factor(ageClass)34.5                                             7.452e-03
## time:factor(ageClass)44.5                                             7.543e-03
## time:factor(ageClass)54.5                                             8.898e-03
## time:factor(ageClass)64.5                                             2.118e-02
## time:factor(ageClass)74.5                                             2.215e-02
## time:factor(ageClass)84.5                                             3.985e-03
## time:factor(ageClass)94.5                                            -2.083e-03
## time:factor(reg_name)Bourgogne-Franche-Comté                          6.228e-03
## time:factor(reg_name)Bretagne                                        -2.416e-02
## time:factor(reg_name)Centre-Val de Loire                              1.709e-02
## time:factor(reg_name)Corse                                           -1.756e-01
## time:factor(reg_name)Grand Est                                       -1.913e-03
## time:factor(reg_name)Guadeloupe                                       1.482e+01
## time:factor(reg_name)Guyane                                          -5.144e-02
## time:factor(reg_name)Hauts-de-France                                 -1.587e-02
## time:factor(reg_name)Île-de-France                                   -2.154e-02
## time:factor(reg_name)La Réunion                                       2.709e-02
## time:factor(reg_name)Martinique                                       2.267e-01
## time:factor(reg_name)Mayotte                                         -4.936e-02
## time:factor(reg_name)Normandie                                        2.722e-04
## time:factor(reg_name)Nouvelle-Aquitaine                              -2.315e-02
## time:factor(reg_name)Occitanie                                        6.928e-03
## time:factor(reg_name)Pays de la Loire                                 2.532e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur                       3.999e-03
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté         -1.788e-01
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté          1.990e-01
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté          4.100e-02
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté         -9.000e-02
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté         -1.143e-01
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté          1.118e-01
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté          1.524e-01
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté          2.405e-01
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté          7.230e-02
## factor(ageClass)14.5:factor(reg_name)Bretagne                        -1.945e-01
## factor(ageClass)24.5:factor(reg_name)Bretagne                        -2.708e-01
## factor(ageClass)34.5:factor(reg_name)Bretagne                        -2.008e-01
## factor(ageClass)44.5:factor(reg_name)Bretagne                         4.305e-02
## factor(ageClass)54.5:factor(reg_name)Bretagne                         4.058e-02
## factor(ageClass)64.5:factor(reg_name)Bretagne                        -1.127e-01
## factor(ageClass)74.5:factor(reg_name)Bretagne                         1.373e-01
## factor(ageClass)84.5:factor(reg_name)Bretagne                         6.214e-02
## factor(ageClass)94.5:factor(reg_name)Bretagne                         1.337e-01
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire             -3.655e-03
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire              7.279e-02
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire              1.831e-01
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire              2.015e-01
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire              1.548e-01
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire              2.948e-01
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire             -1.207e-01
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire              2.110e-01
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire              4.211e-02
## factor(ageClass)14.5:factor(reg_name)Corse                           -2.492e+00
## factor(ageClass)24.5:factor(reg_name)Corse                           -1.901e+00
## factor(ageClass)34.5:factor(reg_name)Corse                           -2.200e+00
## factor(ageClass)44.5:factor(reg_name)Corse                           -1.425e+00
## factor(ageClass)54.5:factor(reg_name)Corse                           -1.302e+00
## factor(ageClass)64.5:factor(reg_name)Corse                           -1.611e+00
## factor(ageClass)74.5:factor(reg_name)Corse                           -1.587e+00
## factor(ageClass)84.5:factor(reg_name)Corse                           -5.760e-01
## factor(ageClass)94.5:factor(reg_name)Corse                            1.307e+01
## factor(ageClass)14.5:factor(reg_name)Grand Est                       -2.821e-01
## factor(ageClass)24.5:factor(reg_name)Grand Est                        1.975e-01
## factor(ageClass)34.5:factor(reg_name)Grand Est                        1.894e-01
## factor(ageClass)44.5:factor(reg_name)Grand Est                        2.051e-01
## factor(ageClass)54.5:factor(reg_name)Grand Est                        2.888e-01
## factor(ageClass)64.5:factor(reg_name)Grand Est                        4.306e-01
## factor(ageClass)74.5:factor(reg_name)Grand Est                        1.793e-01
## factor(ageClass)84.5:factor(reg_name)Grand Est                        2.118e-01
## factor(ageClass)94.5:factor(reg_name)Grand Est                        3.312e-01
## factor(ageClass)14.5:factor(reg_name)Guadeloupe                       1.634e+02
## factor(ageClass)24.5:factor(reg_name)Guadeloupe                       1.642e+02
## factor(ageClass)34.5:factor(reg_name)Guadeloupe                       1.627e+02
## factor(ageClass)44.5:factor(reg_name)Guadeloupe                       1.645e+02
## factor(ageClass)54.5:factor(reg_name)Guadeloupe                       1.640e+02
## factor(ageClass)64.5:factor(reg_name)Guadeloupe                       1.629e+02
## factor(ageClass)74.5:factor(reg_name)Guadeloupe                       1.662e+02
## factor(ageClass)84.5:factor(reg_name)Guadeloupe                       1.824e+02
## factor(ageClass)94.5:factor(reg_name)Guadeloupe                              NA
## factor(ageClass)14.5:factor(reg_name)Guyane                          -8.620e-01
## factor(ageClass)24.5:factor(reg_name)Guyane                           1.703e+01
## factor(ageClass)34.5:factor(reg_name)Guyane                          -5.027e+01
## factor(ageClass)44.5:factor(reg_name)Guyane                           1.906e+01
## factor(ageClass)54.5:factor(reg_name)Guyane                           2.471e+01
## factor(ageClass)64.5:factor(reg_name)Guyane                           3.717e-01
## factor(ageClass)74.5:factor(reg_name)Guyane                                  NA
## factor(ageClass)84.5:factor(reg_name)Guyane                           9.681e-01
## factor(ageClass)94.5:factor(reg_name)Guyane                                  NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France                 -1.881e-01
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France                  6.888e-02
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France                  9.802e-02
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France                  7.353e-02
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France                  1.498e-01
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France                  3.101e-01
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France                  2.925e-01
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France                  3.441e-01
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France                  3.465e-01
## factor(ageClass)14.5:factor(reg_name)Île-de-France                   -2.010e-02
## factor(ageClass)24.5:factor(reg_name)Île-de-France                   -8.495e-02
## factor(ageClass)34.5:factor(reg_name)Île-de-France                    7.803e-02
## factor(ageClass)44.5:factor(reg_name)Île-de-France                    1.346e-01
## factor(ageClass)54.5:factor(reg_name)Île-de-France                    1.450e-01
## factor(ageClass)64.5:factor(reg_name)Île-de-France                    2.914e-01
## factor(ageClass)74.5:factor(reg_name)Île-de-France                    9.173e-02
## factor(ageClass)84.5:factor(reg_name)Île-de-France                   -2.640e-01
## factor(ageClass)94.5:factor(reg_name)Île-de-France                   -6.607e-02
## factor(ageClass)14.5:factor(reg_name)La Réunion                       1.009e+00
## factor(ageClass)24.5:factor(reg_name)La Réunion                      -1.447e+00
## factor(ageClass)34.5:factor(reg_name)La Réunion                       1.421e+00
## factor(ageClass)44.5:factor(reg_name)La Réunion                       1.346e+00
## factor(ageClass)54.5:factor(reg_name)La Réunion                       1.448e+00
## factor(ageClass)64.5:factor(reg_name)La Réunion                       3.103e+00
## factor(ageClass)74.5:factor(reg_name)La Réunion                       2.915e+00
## factor(ageClass)84.5:factor(reg_name)La Réunion                      -1.471e+01
## factor(ageClass)94.5:factor(reg_name)La Réunion                      -1.536e+01
## factor(ageClass)14.5:factor(reg_name)Martinique                       2.559e+00
## factor(ageClass)24.5:factor(reg_name)Martinique                       4.083e+00
## factor(ageClass)34.5:factor(reg_name)Martinique                       3.588e+00
## factor(ageClass)44.5:factor(reg_name)Martinique                       1.977e+00
## factor(ageClass)54.5:factor(reg_name)Martinique                       3.713e+00
## factor(ageClass)64.5:factor(reg_name)Martinique                       2.931e+00
## factor(ageClass)74.5:factor(reg_name)Martinique                       4.360e+00
## factor(ageClass)84.5:factor(reg_name)Martinique                      -5.597e+00
## factor(ageClass)94.5:factor(reg_name)Martinique                       2.864e+00
## factor(ageClass)14.5:factor(reg_name)Mayotte                         -3.947e+01
## factor(ageClass)24.5:factor(reg_name)Mayotte                         -4.009e+01
## factor(ageClass)34.5:factor(reg_name)Mayotte                         -3.980e+01
## factor(ageClass)44.5:factor(reg_name)Mayotte                         -4.000e+01
## factor(ageClass)54.5:factor(reg_name)Mayotte                         -4.010e+01
## factor(ageClass)64.5:factor(reg_name)Mayotte                         -2.478e+01
## factor(ageClass)74.5:factor(reg_name)Mayotte                         -3.841e+01
## factor(ageClass)84.5:factor(reg_name)Mayotte                                 NA
## factor(ageClass)94.5:factor(reg_name)Mayotte                                 NA
## factor(ageClass)14.5:factor(reg_name)Normandie                       -4.497e-02
## factor(ageClass)24.5:factor(reg_name)Normandie                        1.325e-01
## factor(ageClass)34.5:factor(reg_name)Normandie                       -2.421e-01
## factor(ageClass)44.5:factor(reg_name)Normandie                        1.924e-01
## factor(ageClass)54.5:factor(reg_name)Normandie                        1.877e-01
## factor(ageClass)64.5:factor(reg_name)Normandie                        3.366e-01
## factor(ageClass)74.5:factor(reg_name)Normandie                        8.041e-02
## factor(ageClass)84.5:factor(reg_name)Normandie                        1.018e-01
## factor(ageClass)94.5:factor(reg_name)Normandie                       -4.715e-02
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine              -1.887e-01
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine              -2.545e-01
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine              -3.946e-01
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine              -1.313e-01
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine              -3.995e-01
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine               1.504e-02
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine              -4.278e-01
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine              -4.002e-01
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine              -8.593e-01
## factor(ageClass)14.5:factor(reg_name)Occitanie                       -1.324e-01
## factor(ageClass)24.5:factor(reg_name)Occitanie                        6.181e-02
## factor(ageClass)34.5:factor(reg_name)Occitanie                        1.343e-01
## factor(ageClass)44.5:factor(reg_name)Occitanie                        5.576e-02
## factor(ageClass)54.5:factor(reg_name)Occitanie                       -4.864e-02
## factor(ageClass)64.5:factor(reg_name)Occitanie                        1.125e-01
## factor(ageClass)74.5:factor(reg_name)Occitanie                        8.985e-02
## factor(ageClass)84.5:factor(reg_name)Occitanie                        2.944e-01
## factor(ageClass)94.5:factor(reg_name)Occitanie                        4.684e-01
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire                -2.459e-03
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire                 6.938e-02
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire                 1.088e-01
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire                 3.059e-01
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire                 3.352e-01
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire                 4.425e-01
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire                 4.095e-01
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire                 6.909e-01
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire                 7.200e-01
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -2.526e-01
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -1.770e-01
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -9.616e-02
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -1.800e-01
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -6.069e-02
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur       1.360e-01
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -4.271e-01
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -2.201e-01
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur      -2.505e-01
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté     2.342e-02
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté    -1.631e-02
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté    -6.313e-03
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté     1.157e-02
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté     1.391e-02
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté    -2.512e-03
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté    -3.080e-03
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté    -1.621e-02
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté     2.994e-02
## time:factor(ageClass)14.5:factor(reg_name)Bretagne                    2.442e-02
## time:factor(ageClass)24.5:factor(reg_name)Bretagne                    5.557e-02
## time:factor(ageClass)34.5:factor(reg_name)Bretagne                    1.689e-02
## time:factor(ageClass)44.5:factor(reg_name)Bretagne                    9.613e-03
## time:factor(ageClass)54.5:factor(reg_name)Bretagne                    1.703e-02
## time:factor(ageClass)64.5:factor(reg_name)Bretagne                    1.699e-02
## time:factor(ageClass)74.5:factor(reg_name)Bretagne                    6.362e-03
## time:factor(ageClass)84.5:factor(reg_name)Bretagne                    4.643e-02
## time:factor(ageClass)94.5:factor(reg_name)Bretagne                    5.496e-02
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire         7.582e-03
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire        -2.590e-02
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire        -3.447e-02
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire        -2.766e-02
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire        -2.116e-02
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire        -3.703e-02
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire         1.531e-02
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire        -1.176e-02
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire         2.228e-02
## time:factor(ageClass)14.5:factor(reg_name)Corse                       2.007e-01
## time:factor(ageClass)24.5:factor(reg_name)Corse                       1.635e-01
## time:factor(ageClass)34.5:factor(reg_name)Corse                       2.035e-01
## time:factor(ageClass)44.5:factor(reg_name)Corse                       1.010e-01
## time:factor(ageClass)54.5:factor(reg_name)Corse                       1.257e-01
## time:factor(ageClass)64.5:factor(reg_name)Corse                       1.922e-01
## time:factor(ageClass)74.5:factor(reg_name)Corse                       1.818e-01
## time:factor(ageClass)84.5:factor(reg_name)Corse                       8.291e-02
## time:factor(ageClass)94.5:factor(reg_name)Corse                      -6.688e-01
## time:factor(ageClass)14.5:factor(reg_name)Grand Est                   3.855e-02
## time:factor(ageClass)24.5:factor(reg_name)Grand Est                   1.023e-02
## time:factor(ageClass)34.5:factor(reg_name)Grand Est                  -5.719e-03
## time:factor(ageClass)44.5:factor(reg_name)Grand Est                  -2.592e-03
## time:factor(ageClass)54.5:factor(reg_name)Grand Est                  -1.161e-02
## time:factor(ageClass)64.5:factor(reg_name)Grand Est                  -8.163e-03
## time:factor(ageClass)74.5:factor(reg_name)Grand Est                  -6.686e-04
## time:factor(ageClass)84.5:factor(reg_name)Grand Est                   2.883e-02
## time:factor(ageClass)94.5:factor(reg_name)Grand Est                   2.131e-02
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe                 -1.471e+01
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe                 -1.471e+01
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe                 -1.463e+01
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe                 -1.485e+01
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe                 -1.483e+01
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe                 -1.468e+01
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe                 -1.505e+01
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe                 -1.487e+01
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe                         NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane                      4.647e-02
## time:factor(ageClass)24.5:factor(reg_name)Guyane                      1.713e-01
## time:factor(ageClass)34.5:factor(reg_name)Guyane                      1.380e+01
## time:factor(ageClass)44.5:factor(reg_name)Guyane                      1.067e-01
## time:factor(ageClass)54.5:factor(reg_name)Guyane                     -3.912e-01
## time:factor(ageClass)64.5:factor(reg_name)Guyane                      2.184e-02
## time:factor(ageClass)74.5:factor(reg_name)Guyane                             NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane                     -3.985e-03
## time:factor(ageClass)94.5:factor(reg_name)Guyane                             NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France             3.784e-02
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France             9.383e-03
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France            -6.677e-04
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France             3.555e-03
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France             5.038e-03
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France            -1.350e-02
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France            -1.529e-02
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France            -1.678e-03
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France             2.214e-02
## time:factor(ageClass)14.5:factor(reg_name)Île-de-France               7.865e-03
## time:factor(ageClass)24.5:factor(reg_name)Île-de-France               1.240e-02
## time:factor(ageClass)34.5:factor(reg_name)Île-de-France              -5.554e-03
## time:factor(ageClass)44.5:factor(reg_name)Île-de-France              -7.092e-03
## time:factor(ageClass)54.5:factor(reg_name)Île-de-France              -7.372e-03
## time:factor(ageClass)64.5:factor(reg_name)Île-de-France              -1.357e-02
## time:factor(ageClass)74.5:factor(reg_name)Île-de-France              -6.839e-04
## time:factor(ageClass)84.5:factor(reg_name)Île-de-France               4.661e-02
## time:factor(ageClass)94.5:factor(reg_name)Île-de-France               3.542e-02
## time:factor(ageClass)14.5:factor(reg_name)La Réunion                 -7.867e-02
## time:factor(ageClass)24.5:factor(reg_name)La Réunion                  8.907e-02
## time:factor(ageClass)34.5:factor(reg_name)La Réunion                 -1.188e-01
## time:factor(ageClass)44.5:factor(reg_name)La Réunion                 -1.240e-01
## time:factor(ageClass)54.5:factor(reg_name)La Réunion                 -1.187e-01
## time:factor(ageClass)64.5:factor(reg_name)La Réunion                 -2.292e-01
## time:factor(ageClass)74.5:factor(reg_name)La Réunion                 -6.062e-01
## time:factor(ageClass)84.5:factor(reg_name)La Réunion                 -1.363e-01
## time:factor(ageClass)94.5:factor(reg_name)La Réunion                         NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique                 -1.595e-01
## time:factor(ageClass)24.5:factor(reg_name)Martinique                 -2.394e-01
## time:factor(ageClass)34.5:factor(reg_name)Martinique                 -2.756e-01
## time:factor(ageClass)44.5:factor(reg_name)Martinique                 -5.708e-02
## time:factor(ageClass)54.5:factor(reg_name)Martinique                 -2.884e-01
## time:factor(ageClass)64.5:factor(reg_name)Martinique                 -2.394e-01
## time:factor(ageClass)74.5:factor(reg_name)Martinique                 -4.780e-01
## time:factor(ageClass)84.5:factor(reg_name)Martinique                  2.186e+00
## time:factor(ageClass)94.5:factor(reg_name)Martinique                 -1.919e-01
## time:factor(ageClass)14.5:factor(reg_name)Mayotte                     1.163e-01
## time:factor(ageClass)24.5:factor(reg_name)Mayotte                     1.284e-01
## time:factor(ageClass)34.5:factor(reg_name)Mayotte                     6.187e-02
## time:factor(ageClass)44.5:factor(reg_name)Mayotte                     8.733e-02
## time:factor(ageClass)54.5:factor(reg_name)Mayotte                     1.289e-01
## time:factor(ageClass)64.5:factor(reg_name)Mayotte                     2.115e-02
## time:factor(ageClass)74.5:factor(reg_name)Mayotte                     4.768e-02
## time:factor(ageClass)84.5:factor(reg_name)Mayotte                            NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte                            NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie                   3.327e-02
## time:factor(ageClass)24.5:factor(reg_name)Normandie                   1.468e-02
## time:factor(ageClass)34.5:factor(reg_name)Normandie                   4.344e-02
## time:factor(ageClass)44.5:factor(reg_name)Normandie                   1.516e-02
## time:factor(ageClass)54.5:factor(reg_name)Normandie                   1.055e-02
## time:factor(ageClass)64.5:factor(reg_name)Normandie                  -2.129e-02
## time:factor(ageClass)74.5:factor(reg_name)Normandie                   1.395e-02
## time:factor(ageClass)84.5:factor(reg_name)Normandie                   4.524e-02
## time:factor(ageClass)94.5:factor(reg_name)Normandie                   5.840e-02
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine          4.397e-02
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine          3.781e-02
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine          3.038e-02
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine          2.019e-02
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine          3.983e-02
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine         -2.297e-04
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine          2.283e-02
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine          4.758e-02
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine          4.579e-02
## time:factor(ageClass)14.5:factor(reg_name)Occitanie                   9.375e-03
## time:factor(ageClass)24.5:factor(reg_name)Occitanie                  -1.093e-02
## time:factor(ageClass)34.5:factor(reg_name)Occitanie                  -1.130e-02
## time:factor(ageClass)44.5:factor(reg_name)Occitanie                  -1.081e-02
## time:factor(ageClass)54.5:factor(reg_name)Occitanie                   1.084e-03
## time:factor(ageClass)64.5:factor(reg_name)Occitanie                  -2.105e-02
## time:factor(ageClass)74.5:factor(reg_name)Occitanie                  -1.978e-02
## time:factor(ageClass)84.5:factor(reg_name)Occitanie                  -9.939e-03
## time:factor(ageClass)94.5:factor(reg_name)Occitanie                  -3.939e-02
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire            1.146e-02
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire            1.086e-02
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire            3.081e-04
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire           -1.713e-02
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire           -1.275e-02
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire           -3.097e-02
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire           -1.852e-02
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire           -2.788e-02
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire           -5.074e-02
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur  2.839e-02
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur  9.332e-03
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur  4.271e-04
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur  1.097e-02
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur  9.327e-03
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur -5.555e-03
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur  2.321e-02
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur  4.253e-02
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur  3.943e-02
##                                                                      Std. Error
## (Intercept)                                                           4.188e-02
## time                                                                  4.169e-03
## factor(ageClass)14.5                                                  4.862e-02
## factor(ageClass)24.5                                                  4.822e-02
## factor(ageClass)34.5                                                  4.793e-02
## factor(ageClass)44.5                                                  4.804e-02
## factor(ageClass)54.5                                                  4.816e-02
## factor(ageClass)64.5                                                  5.157e-02
## factor(ageClass)74.5                                                  5.467e-02
## factor(ageClass)84.5                                                  6.083e-02
## factor(ageClass)94.5                                                  7.670e-02
## factor(reg_name)Bourgogne-Franche-Comté                               9.611e-02
## factor(reg_name)Bretagne                                              8.841e-02
## factor(reg_name)Centre-Val de Loire                                   1.075e-01
## factor(reg_name)Corse                                                 4.850e-01
## factor(reg_name)Grand Est                                             6.602e-02
## factor(reg_name)Guadeloupe                                            6.537e+03
## factor(reg_name)Guyane                                                3.327e+03
## factor(reg_name)Hauts-de-France                                       5.497e-02
## factor(reg_name)Île-de-France                                         5.209e-02
## factor(reg_name)La Réunion                                            4.602e-01
## factor(reg_name)Martinique                                            1.599e+00
## factor(reg_name)Mayotte                                               1.378e+04
## factor(reg_name)Normandie                                             8.338e-02
## factor(reg_name)Nouvelle-Aquitaine                                    7.924e-02
## factor(reg_name)Occitanie                                             7.267e-02
## factor(reg_name)Pays de la Loire                                      8.094e-02
## factor(reg_name)Provence-Alpes-Côte d'Azur                            6.378e-02
## time:factor(ageClass)14.5                                             4.861e-03
## time:factor(ageClass)24.5                                             4.795e-03
## time:factor(ageClass)34.5                                             4.793e-03
## time:factor(ageClass)44.5                                             4.807e-03
## time:factor(ageClass)54.5                                             4.827e-03
## time:factor(ageClass)64.5                                             5.154e-03
## time:factor(ageClass)74.5                                             5.479e-03
## time:factor(ageClass)84.5                                             6.146e-03
## time:factor(ageClass)94.5                                             8.022e-03
## time:factor(reg_name)Bourgogne-Franche-Comté                          9.787e-03
## time:factor(reg_name)Bretagne                                         9.381e-03
## time:factor(reg_name)Centre-Val de Loire                              1.065e-02
## time:factor(reg_name)Corse                                            4.109e-02
## time:factor(reg_name)Grand Est                                        6.537e-03
## time:factor(reg_name)Guadeloupe                                       5.943e+02
## time:factor(reg_name)Guyane                                           3.048e+02
## time:factor(reg_name)Hauts-de-France                                  5.470e-03
## time:factor(reg_name)Île-de-France                                    5.172e-03
## time:factor(reg_name)La Réunion                                       3.859e-02
## time:factor(reg_name)Martinique                                       1.471e-01
## time:factor(reg_name)Mayotte                                          1.233e+03
## time:factor(reg_name)Normandie                                        8.319e-03
## time:factor(reg_name)Nouvelle-Aquitaine                               7.760e-03
## time:factor(reg_name)Occitanie                                        7.125e-03
## time:factor(reg_name)Pays de la Loire                                 7.968e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur                       6.596e-03
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté          1.101e-01
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté          1.087e-01
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté          1.092e-01
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté          1.087e-01
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté          1.091e-01
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté          1.130e-01
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté          1.201e-01
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté          1.293e-01
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté          1.584e-01
## factor(ageClass)14.5:factor(reg_name)Bretagne                         1.030e-01
## factor(ageClass)24.5:factor(reg_name)Bretagne                         1.010e-01
## factor(ageClass)34.5:factor(reg_name)Bretagne                         1.033e-01
## factor(ageClass)44.5:factor(reg_name)Bretagne                         1.024e-01
## factor(ageClass)54.5:factor(reg_name)Bretagne                         1.035e-01
## factor(ageClass)64.5:factor(reg_name)Bretagne                         1.137e-01
## factor(ageClass)74.5:factor(reg_name)Bretagne                         1.238e-01
## factor(ageClass)84.5:factor(reg_name)Bretagne                         1.257e-01
## factor(ageClass)94.5:factor(reg_name)Bretagne                         1.535e-01
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire              1.220e-01
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire              1.207e-01
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire              1.207e-01
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire              1.199e-01
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire              1.211e-01
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire              1.244e-01
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire              1.337e-01
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire              1.393e-01
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire              1.624e-01
## factor(ageClass)14.5:factor(reg_name)Corse                            5.266e-01
## factor(ageClass)24.5:factor(reg_name)Corse                            5.178e-01
## factor(ageClass)34.5:factor(reg_name)Corse                            5.031e-01
## factor(ageClass)44.5:factor(reg_name)Corse                            5.154e-01
## factor(ageClass)54.5:factor(reg_name)Corse                            5.107e-01
## factor(ageClass)64.5:factor(reg_name)Corse                            5.109e-01
## factor(ageClass)74.5:factor(reg_name)Corse                            5.313e-01
## factor(ageClass)84.5:factor(reg_name)Corse                            5.665e-01
## factor(ageClass)94.5:factor(reg_name)Corse                            6.615e+00
## factor(ageClass)14.5:factor(reg_name)Grand Est                        7.725e-02
## factor(ageClass)24.5:factor(reg_name)Grand Est                        7.626e-02
## factor(ageClass)34.5:factor(reg_name)Grand Est                        7.617e-02
## factor(ageClass)44.5:factor(reg_name)Grand Est                        7.653e-02
## factor(ageClass)54.5:factor(reg_name)Grand Est                        7.713e-02
## factor(ageClass)64.5:factor(reg_name)Grand Est                        8.261e-02
## factor(ageClass)74.5:factor(reg_name)Grand Est                        9.014e-02
## factor(ageClass)84.5:factor(reg_name)Grand Est                        9.890e-02
## factor(ageClass)94.5:factor(reg_name)Grand Est                        1.270e-01
## factor(ageClass)14.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)24.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)34.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)44.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)54.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)64.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)74.5:factor(reg_name)Guadeloupe                       6.537e+03
## factor(ageClass)84.5:factor(reg_name)Guadeloupe                       7.180e+03
## factor(ageClass)94.5:factor(reg_name)Guadeloupe                              NA
## factor(ageClass)14.5:factor(reg_name)Guyane                           3.900e+03
## factor(ageClass)24.5:factor(reg_name)Guyane                           3.327e+03
## factor(ageClass)34.5:factor(reg_name)Guyane                           3.754e+03
## factor(ageClass)44.5:factor(reg_name)Guyane                           3.327e+03
## factor(ageClass)54.5:factor(reg_name)Guyane                           3.327e+03
## factor(ageClass)64.5:factor(reg_name)Guyane                           5.174e+03
## factor(ageClass)74.5:factor(reg_name)Guyane                                  NA
## factor(ageClass)84.5:factor(reg_name)Guyane                           5.775e+03
## factor(ageClass)94.5:factor(reg_name)Guyane                                  NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France                  6.385e-02
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France                  6.353e-02
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France                  6.304e-02
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France                  6.300e-02
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France                  6.354e-02
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France                  6.769e-02
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France                  7.246e-02
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France                  7.972e-02
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France                  1.026e-01
## factor(ageClass)14.5:factor(reg_name)Île-de-France                    6.053e-02
## factor(ageClass)24.5:factor(reg_name)Île-de-France                    5.939e-02
## factor(ageClass)34.5:factor(reg_name)Île-de-France                    5.916e-02
## factor(ageClass)44.5:factor(reg_name)Île-de-France                    5.930e-02
## factor(ageClass)54.5:factor(reg_name)Île-de-France                    5.976e-02
## factor(ageClass)64.5:factor(reg_name)Île-de-France                    6.343e-02
## factor(ageClass)74.5:factor(reg_name)Île-de-France                    6.883e-02
## factor(ageClass)84.5:factor(reg_name)Île-de-France                    7.657e-02
## factor(ageClass)94.5:factor(reg_name)Île-de-France                    9.804e-02
## factor(ageClass)14.5:factor(reg_name)La Réunion                       5.143e-01
## factor(ageClass)24.5:factor(reg_name)La Réunion                       6.712e-01
## factor(ageClass)34.5:factor(reg_name)La Réunion                       5.019e-01
## factor(ageClass)44.5:factor(reg_name)La Réunion                       5.050e-01
## factor(ageClass)54.5:factor(reg_name)La Réunion                       5.076e-01
## factor(ageClass)64.5:factor(reg_name)La Réunion                       5.180e-01
## factor(ageClass)74.5:factor(reg_name)La Réunion                       7.780e-01
## factor(ageClass)84.5:factor(reg_name)La Réunion                       2.192e+03
## factor(ageClass)94.5:factor(reg_name)La Réunion                       6.523e+03
## factor(ageClass)14.5:factor(reg_name)Martinique                       1.674e+00
## factor(ageClass)24.5:factor(reg_name)Martinique                       1.640e+00
## factor(ageClass)34.5:factor(reg_name)Martinique                       1.639e+00
## factor(ageClass)44.5:factor(reg_name)Martinique                       1.645e+00
## factor(ageClass)54.5:factor(reg_name)Martinique                       1.625e+00
## factor(ageClass)64.5:factor(reg_name)Martinique                       1.648e+00
## factor(ageClass)74.5:factor(reg_name)Martinique                       1.690e+00
## factor(ageClass)84.5:factor(reg_name)Martinique                       4.703e+00
## factor(ageClass)94.5:factor(reg_name)Martinique                       1.883e+00
## factor(ageClass)14.5:factor(reg_name)Mayotte                          1.402e+04
## factor(ageClass)24.5:factor(reg_name)Mayotte                          1.390e+04
## factor(ageClass)34.5:factor(reg_name)Mayotte                          1.392e+04
## factor(ageClass)44.5:factor(reg_name)Mayotte                          1.393e+04
## factor(ageClass)54.5:factor(reg_name)Mayotte                          1.393e+04
## factor(ageClass)64.5:factor(reg_name)Mayotte                          1.378e+04
## factor(ageClass)74.5:factor(reg_name)Mayotte                          1.405e+04
## factor(ageClass)84.5:factor(reg_name)Mayotte                                 NA
## factor(ageClass)94.5:factor(reg_name)Mayotte                                 NA
## factor(ageClass)14.5:factor(reg_name)Normandie                        9.595e-02
## factor(ageClass)24.5:factor(reg_name)Normandie                        9.687e-02
## factor(ageClass)34.5:factor(reg_name)Normandie                        9.626e-02
## factor(ageClass)44.5:factor(reg_name)Normandie                        9.539e-02
## factor(ageClass)54.5:factor(reg_name)Normandie                        9.609e-02
## factor(ageClass)64.5:factor(reg_name)Normandie                        1.004e-01
## factor(ageClass)74.5:factor(reg_name)Normandie                        1.082e-01
## factor(ageClass)84.5:factor(reg_name)Normandie                        1.193e-01
## factor(ageClass)94.5:factor(reg_name)Normandie                        1.582e-01
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine               9.167e-02
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine               9.026e-02
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine               9.064e-02
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine               9.032e-02
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine               9.131e-02
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine               9.584e-02
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine               1.044e-01
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine               1.126e-01
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine               1.470e-01
## factor(ageClass)14.5:factor(reg_name)Occitanie                        8.296e-02
## factor(ageClass)24.5:factor(reg_name)Occitanie                        8.174e-02
## factor(ageClass)34.5:factor(reg_name)Occitanie                        8.169e-02
## factor(ageClass)44.5:factor(reg_name)Occitanie                        8.179e-02
## factor(ageClass)54.5:factor(reg_name)Occitanie                        8.190e-02
## factor(ageClass)64.5:factor(reg_name)Occitanie                        8.624e-02
## factor(ageClass)74.5:factor(reg_name)Occitanie                        9.095e-02
## factor(ageClass)84.5:factor(reg_name)Occitanie                        9.567e-02
## factor(ageClass)94.5:factor(reg_name)Occitanie                        1.111e-01
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire                 9.212e-02
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire                 9.173e-02
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire                 9.237e-02
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire                 9.183e-02
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire                 9.241e-02
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire                 9.785e-02
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire                 1.050e-01
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire                 1.116e-01
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire                 1.335e-01
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.281e-02
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.217e-02
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.161e-02
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.146e-02
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.172e-02
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.535e-02
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur       7.969e-02
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur       8.629e-02
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur       1.038e-01
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté     1.108e-02
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté     1.097e-02
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté     1.106e-02
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté     1.104e-02
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté     1.102e-02
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté     1.144e-02
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté     1.208e-02
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté     1.322e-02
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté     1.667e-02
## time:factor(ageClass)14.5:factor(reg_name)Bretagne                    1.073e-02
## time:factor(ageClass)24.5:factor(reg_name)Bretagne                    1.068e-02
## time:factor(ageClass)34.5:factor(reg_name)Bretagne                    1.092e-02
## time:factor(ageClass)44.5:factor(reg_name)Bretagne                    1.085e-02
## time:factor(ageClass)54.5:factor(reg_name)Bretagne                    1.095e-02
## time:factor(ageClass)64.5:factor(reg_name)Bretagne                    1.189e-02
## time:factor(ageClass)74.5:factor(reg_name)Bretagne                    1.279e-02
## time:factor(ageClass)84.5:factor(reg_name)Bretagne                    1.363e-02
## time:factor(ageClass)94.5:factor(reg_name)Bretagne                    1.696e-02
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire         1.205e-02
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire         1.192e-02
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire         1.192e-02
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire         1.187e-02
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire         1.196e-02
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire         1.226e-02
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire         1.314e-02
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire         1.380e-02
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire         1.631e-02
## time:factor(ageClass)14.5:factor(reg_name)Corse                       4.563e-02
## time:factor(ageClass)24.5:factor(reg_name)Corse                       4.429e-02
## time:factor(ageClass)34.5:factor(reg_name)Corse                       4.365e-02
## time:factor(ageClass)44.5:factor(reg_name)Corse                       4.470e-02
## time:factor(ageClass)54.5:factor(reg_name)Corse                       4.426e-02
## time:factor(ageClass)64.5:factor(reg_name)Corse                       4.478e-02
## time:factor(ageClass)74.5:factor(reg_name)Corse                       4.749e-02
## time:factor(ageClass)84.5:factor(reg_name)Corse                       4.855e-02
## time:factor(ageClass)94.5:factor(reg_name)Corse                       4.163e-01
## time:factor(ageClass)14.5:factor(reg_name)Grand Est                   7.640e-03
## time:factor(ageClass)24.5:factor(reg_name)Grand Est                   7.533e-03
## time:factor(ageClass)34.5:factor(reg_name)Grand Est                   7.527e-03
## time:factor(ageClass)44.5:factor(reg_name)Grand Est                   7.561e-03
## time:factor(ageClass)54.5:factor(reg_name)Grand Est                   7.620e-03
## time:factor(ageClass)64.5:factor(reg_name)Grand Est                   8.116e-03
## time:factor(ageClass)74.5:factor(reg_name)Grand Est                   8.814e-03
## time:factor(ageClass)84.5:factor(reg_name)Grand Est                   9.742e-03
## time:factor(ageClass)94.5:factor(reg_name)Grand Est                   1.276e-02
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe                  5.943e+02
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe                  6.632e+02
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe                         NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane                      3.636e+02
## time:factor(ageClass)24.5:factor(reg_name)Guyane                      3.048e+02
## time:factor(ageClass)34.5:factor(reg_name)Guyane                      4.626e+02
## time:factor(ageClass)44.5:factor(reg_name)Guyane                      3.048e+02
## time:factor(ageClass)54.5:factor(reg_name)Guyane                      3.048e+02
## time:factor(ageClass)64.5:factor(reg_name)Guyane                      1.162e+03
## time:factor(ageClass)74.5:factor(reg_name)Guyane                             NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane                      1.589e+03
## time:factor(ageClass)94.5:factor(reg_name)Guyane                             NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France             6.392e-03
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France             6.328e-03
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France             6.302e-03
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France             6.305e-03
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France             6.370e-03
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France             6.754e-03
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France             7.231e-03
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France             8.052e-03
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France             1.067e-02
## time:factor(ageClass)14.5:factor(reg_name)Île-de-France               6.021e-03
## time:factor(ageClass)24.5:factor(reg_name)Île-de-France               5.896e-03
## time:factor(ageClass)34.5:factor(reg_name)Île-de-France               5.893e-03
## time:factor(ageClass)44.5:factor(reg_name)Île-de-France               5.913e-03
## time:factor(ageClass)54.5:factor(reg_name)Île-de-France               5.963e-03
## time:factor(ageClass)64.5:factor(reg_name)Île-de-France               6.319e-03
## time:factor(ageClass)74.5:factor(reg_name)Île-de-France               6.881e-03
## time:factor(ageClass)84.5:factor(reg_name)Île-de-France               7.722e-03
## time:factor(ageClass)94.5:factor(reg_name)Île-de-France               1.014e-02
## time:factor(ageClass)14.5:factor(reg_name)La Réunion                  4.412e-02
## time:factor(ageClass)24.5:factor(reg_name)La Réunion                  5.245e-02
## time:factor(ageClass)34.5:factor(reg_name)La Réunion                  4.313e-02
## time:factor(ageClass)44.5:factor(reg_name)La Réunion                  4.419e-02
## time:factor(ageClass)54.5:factor(reg_name)La Réunion                  4.375e-02
## time:factor(ageClass)64.5:factor(reg_name)La Réunion                  4.597e-02
## time:factor(ageClass)74.5:factor(reg_name)La Réunion                  1.700e-01
## time:factor(ageClass)84.5:factor(reg_name)La Réunion                  2.114e+02
## time:factor(ageClass)94.5:factor(reg_name)La Réunion                         NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique                  1.591e-01
## time:factor(ageClass)24.5:factor(reg_name)Martinique                  1.522e-01
## time:factor(ageClass)34.5:factor(reg_name)Martinique                  1.511e-01
## time:factor(ageClass)44.5:factor(reg_name)Martinique                  1.542e-01
## time:factor(ageClass)54.5:factor(reg_name)Martinique                  1.498e-01
## time:factor(ageClass)64.5:factor(reg_name)Martinique                  1.517e-01
## time:factor(ageClass)74.5:factor(reg_name)Martinique                  1.618e-01
## time:factor(ageClass)84.5:factor(reg_name)Martinique                  1.284e+00
## time:factor(ageClass)94.5:factor(reg_name)Martinique                  1.712e-01
## time:factor(ageClass)14.5:factor(reg_name)Mayotte                     1.276e+03
## time:factor(ageClass)24.5:factor(reg_name)Mayotte                     1.248e+03
## time:factor(ageClass)34.5:factor(reg_name)Mayotte                     1.249e+03
## time:factor(ageClass)44.5:factor(reg_name)Mayotte                     1.253e+03
## time:factor(ageClass)54.5:factor(reg_name)Mayotte                     1.255e+03
## time:factor(ageClass)64.5:factor(reg_name)Mayotte                     1.233e+03
## time:factor(ageClass)74.5:factor(reg_name)Mayotte                     1.278e+03
## time:factor(ageClass)84.5:factor(reg_name)Mayotte                            NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte                            NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie                   9.619e-03
## time:factor(ageClass)24.5:factor(reg_name)Normandie                   9.635e-03
## time:factor(ageClass)34.5:factor(reg_name)Normandie                   9.663e-03
## time:factor(ageClass)44.5:factor(reg_name)Normandie                   9.552e-03
## time:factor(ageClass)54.5:factor(reg_name)Normandie                   9.574e-03
## time:factor(ageClass)64.5:factor(reg_name)Normandie                   9.969e-03
## time:factor(ageClass)74.5:factor(reg_name)Normandie                   1.070e-02
## time:factor(ageClass)84.5:factor(reg_name)Normandie                   1.180e-02
## time:factor(ageClass)94.5:factor(reg_name)Normandie                   1.554e-02
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine          9.040e-03
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine          8.902e-03
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine          8.968e-03
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine          8.948e-03
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine          9.019e-03
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine          9.423e-03
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine          1.033e-02
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine          1.126e-02
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine          1.487e-02
## time:factor(ageClass)14.5:factor(reg_name)Occitanie                   8.163e-03
## time:factor(ageClass)24.5:factor(reg_name)Occitanie                   8.056e-03
## time:factor(ageClass)34.5:factor(reg_name)Occitanie                   8.086e-03
## time:factor(ageClass)44.5:factor(reg_name)Occitanie                   8.091e-03
## time:factor(ageClass)54.5:factor(reg_name)Occitanie                   8.122e-03
## time:factor(ageClass)64.5:factor(reg_name)Occitanie                   8.553e-03
## time:factor(ageClass)74.5:factor(reg_name)Occitanie                   9.048e-03
## time:factor(ageClass)84.5:factor(reg_name)Occitanie                   9.655e-03
## time:factor(ageClass)94.5:factor(reg_name)Occitanie                   1.182e-02
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire            9.074e-03
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire            9.056e-03
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire            9.151e-03
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire            9.102e-03
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire            9.164e-03
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire            9.666e-03
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire            1.045e-02
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire            1.119e-02
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire            1.415e-02
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.548e-03
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.436e-03
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.417e-03
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.398e-03
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.427e-03
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur  7.777e-03
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur  8.217e-03
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur  8.993e-03
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur  1.106e-02
##                                                                      z value
## (Intercept)                                                           -4.022
## time                                                                  12.340
## factor(ageClass)14.5                                                  -0.108
## factor(ageClass)24.5                                                  -4.166
## factor(ageClass)34.5                                                  -3.678
## factor(ageClass)44.5                                                  -4.329
## factor(ageClass)54.5                                                  -6.784
## factor(ageClass)64.5                                                 -10.830
## factor(ageClass)74.5                                                 -12.264
## factor(ageClass)84.5                                                 -15.916
## factor(ageClass)94.5                                                 -14.693
## factor(reg_name)Bourgogne-Franche-Comté                               -5.526
## factor(reg_name)Bretagne                                               7.300
## factor(reg_name)Centre-Val de Loire                                   -0.225
## factor(reg_name)Corse                                                  5.729
## factor(reg_name)Grand Est                                            -10.009
## factor(reg_name)Guadeloupe                                            -0.025
## factor(reg_name)Guyane                                                -0.006
## factor(reg_name)Hauts-de-France                                        8.754
## factor(reg_name)Île-de-France                                         11.175
## factor(reg_name)La Réunion                                            -6.985
## factor(reg_name)Martinique                                            -1.710
## factor(reg_name)Mayotte                                                0.001
## factor(reg_name)Normandie                                             -1.354
## factor(reg_name)Nouvelle-Aquitaine                                     2.717
## factor(reg_name)Occitanie                                              3.694
## factor(reg_name)Pays de la Loire                                      -2.764
## factor(reg_name)Provence-Alpes-Côte d'Azur                             7.296
## time:factor(ageClass)14.5                                             -2.732
## time:factor(ageClass)24.5                                              0.543
## time:factor(ageClass)34.5                                              1.555
## time:factor(ageClass)44.5                                              1.569
## time:factor(ageClass)54.5                                              1.843
## time:factor(ageClass)64.5                                              4.110
## time:factor(ageClass)74.5                                              4.043
## time:factor(ageClass)84.5                                              0.648
## time:factor(ageClass)94.5                                             -0.260
## time:factor(reg_name)Bourgogne-Franche-Comté                           0.636
## time:factor(reg_name)Bretagne                                         -2.575
## time:factor(reg_name)Centre-Val de Loire                               1.604
## time:factor(reg_name)Corse                                            -4.273
## time:factor(reg_name)Grand Est                                        -0.293
## time:factor(reg_name)Guadeloupe                                        0.025
## time:factor(reg_name)Guyane                                            0.000
## time:factor(reg_name)Hauts-de-France                                  -2.901
## time:factor(reg_name)Île-de-France                                    -4.164
## time:factor(reg_name)La Réunion                                        0.702
## time:factor(reg_name)Martinique                                        1.541
## time:factor(reg_name)Mayotte                                           0.000
## time:factor(reg_name)Normandie                                         0.033
## time:factor(reg_name)Nouvelle-Aquitaine                               -2.983
## time:factor(reg_name)Occitanie                                         0.972
## time:factor(reg_name)Pays de la Loire                                  0.318
## time:factor(reg_name)Provence-Alpes-Côte d'Azur                        0.606
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté          -1.624
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté           1.830
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté           0.376
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté          -0.828
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté          -1.048
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté           0.989
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté           1.269
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté           1.861
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté           0.456
## factor(ageClass)14.5:factor(reg_name)Bretagne                         -1.889
## factor(ageClass)24.5:factor(reg_name)Bretagne                         -2.681
## factor(ageClass)34.5:factor(reg_name)Bretagne                         -1.944
## factor(ageClass)44.5:factor(reg_name)Bretagne                          0.420
## factor(ageClass)54.5:factor(reg_name)Bretagne                          0.392
## factor(ageClass)64.5:factor(reg_name)Bretagne                         -0.992
## factor(ageClass)74.5:factor(reg_name)Bretagne                          1.109
## factor(ageClass)84.5:factor(reg_name)Bretagne                          0.494
## factor(ageClass)94.5:factor(reg_name)Bretagne                          0.871
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire              -0.030
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire               0.603
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire               1.516
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire               1.680
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire               1.279
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire               2.370
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire              -0.903
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire               1.515
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire               0.259
## factor(ageClass)14.5:factor(reg_name)Corse                            -4.732
## factor(ageClass)24.5:factor(reg_name)Corse                            -3.671
## factor(ageClass)34.5:factor(reg_name)Corse                            -4.373
## factor(ageClass)44.5:factor(reg_name)Corse                            -2.764
## factor(ageClass)54.5:factor(reg_name)Corse                            -2.549
## factor(ageClass)64.5:factor(reg_name)Corse                            -3.153
## factor(ageClass)74.5:factor(reg_name)Corse                            -2.987
## factor(ageClass)84.5:factor(reg_name)Corse                            -1.017
## factor(ageClass)94.5:factor(reg_name)Corse                             1.976
## factor(ageClass)14.5:factor(reg_name)Grand Est                        -3.651
## factor(ageClass)24.5:factor(reg_name)Grand Est                         2.590
## factor(ageClass)34.5:factor(reg_name)Grand Est                         2.487
## factor(ageClass)44.5:factor(reg_name)Grand Est                         2.680
## factor(ageClass)54.5:factor(reg_name)Grand Est                         3.744
## factor(ageClass)64.5:factor(reg_name)Grand Est                         5.212
## factor(ageClass)74.5:factor(reg_name)Grand Est                         1.989
## factor(ageClass)84.5:factor(reg_name)Grand Est                         2.142
## factor(ageClass)94.5:factor(reg_name)Grand Est                         2.608
## factor(ageClass)14.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)24.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)34.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)44.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)54.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)64.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)74.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)84.5:factor(reg_name)Guadeloupe                        0.025
## factor(ageClass)94.5:factor(reg_name)Guadeloupe                           NA
## factor(ageClass)14.5:factor(reg_name)Guyane                            0.000
## factor(ageClass)24.5:factor(reg_name)Guyane                            0.005
## factor(ageClass)34.5:factor(reg_name)Guyane                           -0.013
## factor(ageClass)44.5:factor(reg_name)Guyane                            0.006
## factor(ageClass)54.5:factor(reg_name)Guyane                            0.007
## factor(ageClass)64.5:factor(reg_name)Guyane                            0.000
## factor(ageClass)74.5:factor(reg_name)Guyane                               NA
## factor(ageClass)84.5:factor(reg_name)Guyane                            0.000
## factor(ageClass)94.5:factor(reg_name)Guyane                               NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France                  -2.946
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France                   1.084
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France                   1.555
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France                   1.167
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France                   2.357
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France                   4.582
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France                   4.036
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France                   4.316
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France                   3.378
## factor(ageClass)14.5:factor(reg_name)Île-de-France                    -0.332
## factor(ageClass)24.5:factor(reg_name)Île-de-France                    -1.430
## factor(ageClass)34.5:factor(reg_name)Île-de-France                     1.319
## factor(ageClass)44.5:factor(reg_name)Île-de-France                     2.269
## factor(ageClass)54.5:factor(reg_name)Île-de-France                     2.426
## factor(ageClass)64.5:factor(reg_name)Île-de-France                     4.594
## factor(ageClass)74.5:factor(reg_name)Île-de-France                     1.333
## factor(ageClass)84.5:factor(reg_name)Île-de-France                    -3.448
## factor(ageClass)94.5:factor(reg_name)Île-de-France                    -0.674
## factor(ageClass)14.5:factor(reg_name)La Réunion                        1.961
## factor(ageClass)24.5:factor(reg_name)La Réunion                       -2.155
## factor(ageClass)34.5:factor(reg_name)La Réunion                        2.831
## factor(ageClass)44.5:factor(reg_name)La Réunion                        2.664
## factor(ageClass)54.5:factor(reg_name)La Réunion                        2.854
## factor(ageClass)64.5:factor(reg_name)La Réunion                        5.990
## factor(ageClass)74.5:factor(reg_name)La Réunion                        3.746
## factor(ageClass)84.5:factor(reg_name)La Réunion                       -0.007
## factor(ageClass)94.5:factor(reg_name)La Réunion                       -0.002
## factor(ageClass)14.5:factor(reg_name)Martinique                        1.528
## factor(ageClass)24.5:factor(reg_name)Martinique                        2.490
## factor(ageClass)34.5:factor(reg_name)Martinique                        2.189
## factor(ageClass)44.5:factor(reg_name)Martinique                        1.202
## factor(ageClass)54.5:factor(reg_name)Martinique                        2.285
## factor(ageClass)64.5:factor(reg_name)Martinique                        1.778
## factor(ageClass)74.5:factor(reg_name)Martinique                        2.580
## factor(ageClass)84.5:factor(reg_name)Martinique                       -1.190
## factor(ageClass)94.5:factor(reg_name)Martinique                        1.521
## factor(ageClass)14.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)24.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)34.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)44.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)54.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)64.5:factor(reg_name)Mayotte                          -0.002
## factor(ageClass)74.5:factor(reg_name)Mayotte                          -0.003
## factor(ageClass)84.5:factor(reg_name)Mayotte                              NA
## factor(ageClass)94.5:factor(reg_name)Mayotte                              NA
## factor(ageClass)14.5:factor(reg_name)Normandie                        -0.469
## factor(ageClass)24.5:factor(reg_name)Normandie                         1.368
## factor(ageClass)34.5:factor(reg_name)Normandie                        -2.515
## factor(ageClass)44.5:factor(reg_name)Normandie                         2.017
## factor(ageClass)54.5:factor(reg_name)Normandie                         1.953
## factor(ageClass)64.5:factor(reg_name)Normandie                         3.353
## factor(ageClass)74.5:factor(reg_name)Normandie                         0.743
## factor(ageClass)84.5:factor(reg_name)Normandie                         0.853
## factor(ageClass)94.5:factor(reg_name)Normandie                        -0.298
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine               -2.059
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine               -2.820
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine               -4.354
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine               -1.454
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine               -4.375
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine                0.157
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine               -4.096
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine               -3.555
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine               -5.845
## factor(ageClass)14.5:factor(reg_name)Occitanie                        -1.596
## factor(ageClass)24.5:factor(reg_name)Occitanie                         0.756
## factor(ageClass)34.5:factor(reg_name)Occitanie                         1.644
## factor(ageClass)44.5:factor(reg_name)Occitanie                         0.682
## factor(ageClass)54.5:factor(reg_name)Occitanie                        -0.594
## factor(ageClass)64.5:factor(reg_name)Occitanie                         1.304
## factor(ageClass)74.5:factor(reg_name)Occitanie                         0.988
## factor(ageClass)84.5:factor(reg_name)Occitanie                         3.077
## factor(ageClass)94.5:factor(reg_name)Occitanie                         4.217
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire                 -0.027
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire                  0.756
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire                  1.178
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire                  3.332
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire                  3.627
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire                  4.522
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire                  3.901
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire                  6.192
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire                  5.393
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -3.469
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -2.453
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -1.343
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -2.518
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -0.846
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur        1.805
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -5.360
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -2.551
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur       -2.412
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté      2.113
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté     -1.486
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté     -0.571
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté      1.049
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté      1.263
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté     -0.219
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté     -0.255
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté     -1.226
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté      1.796
## time:factor(ageClass)14.5:factor(reg_name)Bretagne                     2.276
## time:factor(ageClass)24.5:factor(reg_name)Bretagne                     5.203
## time:factor(ageClass)34.5:factor(reg_name)Bretagne                     1.547
## time:factor(ageClass)44.5:factor(reg_name)Bretagne                     0.886
## time:factor(ageClass)54.5:factor(reg_name)Bretagne                     1.556
## time:factor(ageClass)64.5:factor(reg_name)Bretagne                     1.429
## time:factor(ageClass)74.5:factor(reg_name)Bretagne                     0.498
## time:factor(ageClass)84.5:factor(reg_name)Bretagne                     3.406
## time:factor(ageClass)94.5:factor(reg_name)Bretagne                     3.242
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire          0.629
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire         -2.174
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire         -2.891
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire         -2.330
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire         -1.770
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire         -3.020
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire          1.165
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire         -0.852
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire          1.366
## time:factor(ageClass)14.5:factor(reg_name)Corse                        4.399
## time:factor(ageClass)24.5:factor(reg_name)Corse                        3.691
## time:factor(ageClass)34.5:factor(reg_name)Corse                        4.662
## time:factor(ageClass)44.5:factor(reg_name)Corse                        2.259
## time:factor(ageClass)54.5:factor(reg_name)Corse                        2.839
## time:factor(ageClass)64.5:factor(reg_name)Corse                        4.292
## time:factor(ageClass)74.5:factor(reg_name)Corse                        3.829
## time:factor(ageClass)84.5:factor(reg_name)Corse                        1.708
## time:factor(ageClass)94.5:factor(reg_name)Corse                       -1.607
## time:factor(ageClass)14.5:factor(reg_name)Grand Est                    5.046
## time:factor(ageClass)24.5:factor(reg_name)Grand Est                    1.358
## time:factor(ageClass)34.5:factor(reg_name)Grand Est                   -0.760
## time:factor(ageClass)44.5:factor(reg_name)Grand Est                   -0.343
## time:factor(ageClass)54.5:factor(reg_name)Grand Est                   -1.524
## time:factor(ageClass)64.5:factor(reg_name)Grand Est                   -1.006
## time:factor(ageClass)74.5:factor(reg_name)Grand Est                   -0.076
## time:factor(ageClass)84.5:factor(reg_name)Grand Est                    2.959
## time:factor(ageClass)94.5:factor(reg_name)Grand Est                    1.671
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe                  -0.025
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe                  -0.022
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe                      NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane                       0.000
## time:factor(ageClass)24.5:factor(reg_name)Guyane                       0.001
## time:factor(ageClass)34.5:factor(reg_name)Guyane                       0.030
## time:factor(ageClass)44.5:factor(reg_name)Guyane                       0.000
## time:factor(ageClass)54.5:factor(reg_name)Guyane                      -0.001
## time:factor(ageClass)64.5:factor(reg_name)Guyane                       0.000
## time:factor(ageClass)74.5:factor(reg_name)Guyane                          NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane                       0.000
## time:factor(ageClass)94.5:factor(reg_name)Guyane                          NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France              5.919
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France              1.483
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France             -0.106
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France              0.564
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France              0.791
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France             -1.998
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France             -2.115
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France             -0.208
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France              2.074
## time:factor(ageClass)14.5:factor(reg_name)Île-de-France                1.306
## time:factor(ageClass)24.5:factor(reg_name)Île-de-France                2.102
## time:factor(ageClass)34.5:factor(reg_name)Île-de-France               -0.943
## time:factor(ageClass)44.5:factor(reg_name)Île-de-France               -1.199
## time:factor(ageClass)54.5:factor(reg_name)Île-de-France               -1.236
## time:factor(ageClass)64.5:factor(reg_name)Île-de-France               -2.148
## time:factor(ageClass)74.5:factor(reg_name)Île-de-France               -0.099
## time:factor(ageClass)84.5:factor(reg_name)Île-de-France                6.036
## time:factor(ageClass)94.5:factor(reg_name)Île-de-France                3.495
## time:factor(ageClass)14.5:factor(reg_name)La Réunion                  -1.783
## time:factor(ageClass)24.5:factor(reg_name)La Réunion                   1.698
## time:factor(ageClass)34.5:factor(reg_name)La Réunion                  -2.754
## time:factor(ageClass)44.5:factor(reg_name)La Réunion                  -2.806
## time:factor(ageClass)54.5:factor(reg_name)La Réunion                  -2.712
## time:factor(ageClass)64.5:factor(reg_name)La Réunion                  -4.987
## time:factor(ageClass)74.5:factor(reg_name)La Réunion                  -3.566
## time:factor(ageClass)84.5:factor(reg_name)La Réunion                  -0.001
## time:factor(ageClass)94.5:factor(reg_name)La Réunion                      NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique                  -1.003
## time:factor(ageClass)24.5:factor(reg_name)Martinique                  -1.573
## time:factor(ageClass)34.5:factor(reg_name)Martinique                  -1.825
## time:factor(ageClass)44.5:factor(reg_name)Martinique                  -0.370
## time:factor(ageClass)54.5:factor(reg_name)Martinique                  -1.925
## time:factor(ageClass)64.5:factor(reg_name)Martinique                  -1.578
## time:factor(ageClass)74.5:factor(reg_name)Martinique                  -2.953
## time:factor(ageClass)84.5:factor(reg_name)Martinique                   1.703
## time:factor(ageClass)94.5:factor(reg_name)Martinique                  -1.121
## time:factor(ageClass)14.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)24.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)34.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)44.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)54.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)64.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)74.5:factor(reg_name)Mayotte                      0.000
## time:factor(ageClass)84.5:factor(reg_name)Mayotte                         NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte                         NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie                    3.459
## time:factor(ageClass)24.5:factor(reg_name)Normandie                    1.524
## time:factor(ageClass)34.5:factor(reg_name)Normandie                    4.495
## time:factor(ageClass)44.5:factor(reg_name)Normandie                    1.587
## time:factor(ageClass)54.5:factor(reg_name)Normandie                    1.102
## time:factor(ageClass)64.5:factor(reg_name)Normandie                   -2.136
## time:factor(ageClass)74.5:factor(reg_name)Normandie                    1.303
## time:factor(ageClass)84.5:factor(reg_name)Normandie                    3.834
## time:factor(ageClass)94.5:factor(reg_name)Normandie                    3.758
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine           4.864
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine           4.248
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine           3.388
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine           2.257
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine           4.417
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine          -0.024
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine           2.211
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine           4.227
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine           3.080
## time:factor(ageClass)14.5:factor(reg_name)Occitanie                    1.148
## time:factor(ageClass)24.5:factor(reg_name)Occitanie                   -1.357
## time:factor(ageClass)34.5:factor(reg_name)Occitanie                   -1.397
## time:factor(ageClass)44.5:factor(reg_name)Occitanie                   -1.336
## time:factor(ageClass)54.5:factor(reg_name)Occitanie                    0.133
## time:factor(ageClass)64.5:factor(reg_name)Occitanie                   -2.461
## time:factor(ageClass)74.5:factor(reg_name)Occitanie                   -2.186
## time:factor(ageClass)84.5:factor(reg_name)Occitanie                   -1.029
## time:factor(ageClass)94.5:factor(reg_name)Occitanie                   -3.333
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire             1.263
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire             1.200
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire             0.034
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire            -1.882
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire            -1.391
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire            -3.204
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire            -1.772
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire            -2.491
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire            -3.586
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur   3.761
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur   1.255
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur   0.058
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur   1.483
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur   1.256
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur  -0.714
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur   2.825
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur   4.729
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur   3.567
##                                                                      Pr(>|z|)
## (Intercept)                                                          5.77e-05
## time                                                                  < 2e-16
## factor(ageClass)14.5                                                 0.914274
## factor(ageClass)24.5                                                 3.11e-05
## factor(ageClass)34.5                                                 0.000235
## factor(ageClass)44.5                                                 1.50e-05
## factor(ageClass)54.5                                                 1.17e-11
## factor(ageClass)64.5                                                  < 2e-16
## factor(ageClass)74.5                                                  < 2e-16
## factor(ageClass)84.5                                                  < 2e-16
## factor(ageClass)94.5                                                  < 2e-16
## factor(reg_name)Bourgogne-Franche-Comté                              3.27e-08
## factor(reg_name)Bretagne                                             2.89e-13
## factor(reg_name)Centre-Val de Loire                                  0.821624
## factor(reg_name)Corse                                                1.01e-08
## factor(reg_name)Grand Est                                             < 2e-16
## factor(reg_name)Guadeloupe                                           0.980137
## factor(reg_name)Guyane                                               0.995588
## factor(reg_name)Hauts-de-France                                       < 2e-16
## factor(reg_name)Île-de-France                                         < 2e-16
## factor(reg_name)La Réunion                                           2.86e-12
## factor(reg_name)Martinique                                           0.087289
## factor(reg_name)Mayotte                                              0.998850
## factor(reg_name)Normandie                                            0.175614
## factor(reg_name)Nouvelle-Aquitaine                                   0.006593
## factor(reg_name)Occitanie                                            0.000221
## factor(reg_name)Pays de la Loire                                     0.005717
## factor(reg_name)Provence-Alpes-Côte d'Azur                           2.97e-13
## time:factor(ageClass)14.5                                            0.006293
## time:factor(ageClass)24.5                                            0.586954
## time:factor(ageClass)34.5                                            0.119980
## time:factor(ageClass)44.5                                            0.116589
## time:factor(ageClass)54.5                                            0.065265
## time:factor(ageClass)64.5                                            3.96e-05
## time:factor(ageClass)74.5                                            5.29e-05
## time:factor(ageClass)84.5                                            0.516734
## time:factor(ageClass)94.5                                            0.795146
## time:factor(reg_name)Bourgogne-Franche-Comté                         0.524547
## time:factor(reg_name)Bretagne                                        0.010011
## time:factor(reg_name)Centre-Val de Loire                             0.108699
## time:factor(reg_name)Corse                                           1.93e-05
## time:factor(reg_name)Grand Est                                       0.769810
## time:factor(reg_name)Guadeloupe                                      0.980101
## time:factor(reg_name)Guyane                                          0.999865
## time:factor(reg_name)Hauts-de-France                                 0.003723
## time:factor(reg_name)Île-de-France                                   3.13e-05
## time:factor(reg_name)La Réunion                                      0.482642
## time:factor(reg_name)Martinique                                      0.123346
## time:factor(reg_name)Mayotte                                         0.999968
## time:factor(reg_name)Normandie                                       0.973897
## time:factor(reg_name)Nouvelle-Aquitaine                              0.002855
## time:factor(reg_name)Occitanie                                       0.330854
## time:factor(reg_name)Pays de la Loire                                0.750614
## time:factor(reg_name)Provence-Alpes-Côte d'Azur                      0.544372
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté         0.104442
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté         0.067190
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté         0.707270
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté         0.407488
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté         0.294796
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté         0.322664
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté         0.204442
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté         0.062764
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté         0.648069
## factor(ageClass)14.5:factor(reg_name)Bretagne                        0.058952
## factor(ageClass)24.5:factor(reg_name)Bretagne                        0.007334
## factor(ageClass)34.5:factor(reg_name)Bretagne                        0.051874
## factor(ageClass)44.5:factor(reg_name)Bretagne                        0.674267
## factor(ageClass)54.5:factor(reg_name)Bretagne                        0.694927
## factor(ageClass)64.5:factor(reg_name)Bretagne                        0.321245
## factor(ageClass)74.5:factor(reg_name)Bretagne                        0.267640
## factor(ageClass)84.5:factor(reg_name)Bretagne                        0.621036
## factor(ageClass)94.5:factor(reg_name)Bretagne                        0.383911
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire             0.976097
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire             0.546474
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire             0.129420
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire             0.092869
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire             0.200906
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire             0.017771
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire             0.366495
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire             0.129785
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire             0.795474
## factor(ageClass)14.5:factor(reg_name)Corse                           2.23e-06
## factor(ageClass)24.5:factor(reg_name)Corse                           0.000241
## factor(ageClass)34.5:factor(reg_name)Corse                           1.23e-05
## factor(ageClass)44.5:factor(reg_name)Corse                           0.005707
## factor(ageClass)54.5:factor(reg_name)Corse                           0.010818
## factor(ageClass)64.5:factor(reg_name)Corse                           0.001613
## factor(ageClass)74.5:factor(reg_name)Corse                           0.002822
## factor(ageClass)84.5:factor(reg_name)Corse                           0.309220
## factor(ageClass)94.5:factor(reg_name)Corse                           0.048140
## factor(ageClass)14.5:factor(reg_name)Grand Est                       0.000261
## factor(ageClass)24.5:factor(reg_name)Grand Est                       0.009603
## factor(ageClass)34.5:factor(reg_name)Grand Est                       0.012898
## factor(ageClass)44.5:factor(reg_name)Grand Est                       0.007367
## factor(ageClass)54.5:factor(reg_name)Grand Est                       0.000181
## factor(ageClass)64.5:factor(reg_name)Grand Est                       1.87e-07
## factor(ageClass)74.5:factor(reg_name)Grand Est                       0.046682
## factor(ageClass)84.5:factor(reg_name)Grand Est                       0.032226
## factor(ageClass)94.5:factor(reg_name)Grand Est                       0.009094
## factor(ageClass)14.5:factor(reg_name)Guadeloupe                      0.980055
## factor(ageClass)24.5:factor(reg_name)Guadeloupe                      0.979962
## factor(ageClass)34.5:factor(reg_name)Guadeloupe                      0.980142
## factor(ageClass)44.5:factor(reg_name)Guadeloupe                      0.979917
## factor(ageClass)54.5:factor(reg_name)Guadeloupe                      0.979981
## factor(ageClass)64.5:factor(reg_name)Guadeloupe                      0.980116
## factor(ageClass)74.5:factor(reg_name)Guadeloupe                      0.979715
## factor(ageClass)84.5:factor(reg_name)Guadeloupe                      0.979728
## factor(ageClass)94.5:factor(reg_name)Guadeloupe                            NA
## factor(ageClass)14.5:factor(reg_name)Guyane                          0.999824
## factor(ageClass)24.5:factor(reg_name)Guyane                          0.995917
## factor(ageClass)34.5:factor(reg_name)Guyane                          0.989317
## factor(ageClass)44.5:factor(reg_name)Guyane                          0.995430
## factor(ageClass)54.5:factor(reg_name)Guyane                          0.994075
## factor(ageClass)64.5:factor(reg_name)Guyane                          0.999943
## factor(ageClass)74.5:factor(reg_name)Guyane                                NA
## factor(ageClass)84.5:factor(reg_name)Guyane                          0.999866
## factor(ageClass)94.5:factor(reg_name)Guyane                                NA
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France                 0.003215
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France                 0.278257
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France                 0.119951
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France                 0.243209
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France                 0.018404
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France                 4.62e-06
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France                 5.43e-05
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France                 1.59e-05
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France                 0.000730
## factor(ageClass)14.5:factor(reg_name)Île-de-France                   0.739777
## factor(ageClass)24.5:factor(reg_name)Île-de-France                   0.152624
## factor(ageClass)34.5:factor(reg_name)Île-de-France                   0.187128
## factor(ageClass)44.5:factor(reg_name)Île-de-France                   0.023245
## factor(ageClass)54.5:factor(reg_name)Île-de-France                   0.015278
## factor(ageClass)64.5:factor(reg_name)Île-de-France                   4.35e-06
## factor(ageClass)74.5:factor(reg_name)Île-de-France                   0.182613
## factor(ageClass)84.5:factor(reg_name)Île-de-France                   0.000565
## factor(ageClass)94.5:factor(reg_name)Île-de-France                   0.500388
## factor(ageClass)14.5:factor(reg_name)La Réunion                      0.049861
## factor(ageClass)24.5:factor(reg_name)La Réunion                      0.031129
## factor(ageClass)34.5:factor(reg_name)La Réunion                      0.004645
## factor(ageClass)44.5:factor(reg_name)La Réunion                      0.007711
## factor(ageClass)54.5:factor(reg_name)La Réunion                      0.004322
## factor(ageClass)64.5:factor(reg_name)La Réunion                      2.10e-09
## factor(ageClass)74.5:factor(reg_name)La Réunion                      0.000179
## factor(ageClass)84.5:factor(reg_name)La Réunion                      0.994644
## factor(ageClass)94.5:factor(reg_name)La Réunion                      0.998122
## factor(ageClass)14.5:factor(reg_name)Martinique                      0.126434
## factor(ageClass)24.5:factor(reg_name)Martinique                      0.012768
## factor(ageClass)34.5:factor(reg_name)Martinique                      0.028591
## factor(ageClass)44.5:factor(reg_name)Martinique                      0.229297
## factor(ageClass)54.5:factor(reg_name)Martinique                      0.022340
## factor(ageClass)64.5:factor(reg_name)Martinique                      0.075373
## factor(ageClass)74.5:factor(reg_name)Martinique                      0.009873
## factor(ageClass)84.5:factor(reg_name)Martinique                      0.233965
## factor(ageClass)94.5:factor(reg_name)Martinique                      0.128267
## factor(ageClass)14.5:factor(reg_name)Mayotte                         0.997754
## factor(ageClass)24.5:factor(reg_name)Mayotte                         0.997700
## factor(ageClass)34.5:factor(reg_name)Mayotte                         0.997719
## factor(ageClass)44.5:factor(reg_name)Mayotte                         0.997710
## factor(ageClass)54.5:factor(reg_name)Mayotte                         0.997704
## factor(ageClass)64.5:factor(reg_name)Mayotte                         0.998565
## factor(ageClass)74.5:factor(reg_name)Mayotte                         0.997818
## factor(ageClass)84.5:factor(reg_name)Mayotte                               NA
## factor(ageClass)94.5:factor(reg_name)Mayotte                               NA
## factor(ageClass)14.5:factor(reg_name)Normandie                       0.639266
## factor(ageClass)24.5:factor(reg_name)Normandie                       0.171262
## factor(ageClass)34.5:factor(reg_name)Normandie                       0.011895
## factor(ageClass)44.5:factor(reg_name)Normandie                       0.043725
## factor(ageClass)54.5:factor(reg_name)Normandie                       0.050841
## factor(ageClass)64.5:factor(reg_name)Normandie                       0.000799
## factor(ageClass)74.5:factor(reg_name)Normandie                       0.457475
## factor(ageClass)84.5:factor(reg_name)Normandie                       0.393435
## factor(ageClass)94.5:factor(reg_name)Normandie                       0.765608
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine              0.039518
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine              0.004810
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine              1.34e-05
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine              0.146026
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine              1.22e-05
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine              0.875290
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine              4.21e-05
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine              0.000377
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine              5.07e-09
## factor(ageClass)14.5:factor(reg_name)Occitanie                       0.110488
## factor(ageClass)24.5:factor(reg_name)Occitanie                       0.449529
## factor(ageClass)34.5:factor(reg_name)Occitanie                       0.100267
## factor(ageClass)44.5:factor(reg_name)Occitanie                       0.495442
## factor(ageClass)54.5:factor(reg_name)Occitanie                       0.552621
## factor(ageClass)64.5:factor(reg_name)Occitanie                       0.192232
## factor(ageClass)74.5:factor(reg_name)Occitanie                       0.323188
## factor(ageClass)84.5:factor(reg_name)Occitanie                       0.002089
## factor(ageClass)94.5:factor(reg_name)Occitanie                       2.47e-05
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire                0.978700
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire                0.449411
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire                0.238756
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire                0.000863
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire                0.000287
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire                6.12e-06
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire                9.56e-05
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire                5.93e-10
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire                6.91e-08
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.000522
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.014167
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.179320
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.011786
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.397408
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.071111
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur      8.33e-08
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.010754
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur      0.015861
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté    0.034639
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté    0.137256
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté    0.568178
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté    0.294276
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté    0.206623
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté    0.826264
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté    0.798678
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté    0.220199
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté    0.072536
## time:factor(ageClass)14.5:factor(reg_name)Bretagne                   0.022863
## time:factor(ageClass)24.5:factor(reg_name)Bretagne                   1.96e-07
## time:factor(ageClass)34.5:factor(reg_name)Bretagne                   0.121918
## time:factor(ageClass)44.5:factor(reg_name)Bretagne                   0.375443
## time:factor(ageClass)54.5:factor(reg_name)Bretagne                   0.119680
## time:factor(ageClass)64.5:factor(reg_name)Bretagne                   0.152885
## time:factor(ageClass)74.5:factor(reg_name)Bretagne                   0.618749
## time:factor(ageClass)84.5:factor(reg_name)Bretagne                   0.000659
## time:factor(ageClass)94.5:factor(reg_name)Bretagne                   0.001188
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire        0.529128
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire        0.029737
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire        0.003846
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire        0.019818
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire        0.076800
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire        0.002531
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire        0.243975
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire        0.394145
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire        0.172009
## time:factor(ageClass)14.5:factor(reg_name)Corse                      1.09e-05
## time:factor(ageClass)24.5:factor(reg_name)Corse                      0.000223
## time:factor(ageClass)34.5:factor(reg_name)Corse                      3.14e-06
## time:factor(ageClass)44.5:factor(reg_name)Corse                      0.023887
## time:factor(ageClass)54.5:factor(reg_name)Corse                      0.004523
## time:factor(ageClass)64.5:factor(reg_name)Corse                      1.77e-05
## time:factor(ageClass)74.5:factor(reg_name)Corse                      0.000129
## time:factor(ageClass)84.5:factor(reg_name)Corse                      0.087697
## time:factor(ageClass)94.5:factor(reg_name)Corse                      0.108159
## time:factor(ageClass)14.5:factor(reg_name)Grand Est                  4.52e-07
## time:factor(ageClass)24.5:factor(reg_name)Grand Est                  0.174550
## time:factor(ageClass)34.5:factor(reg_name)Grand Est                  0.447357
## time:factor(ageClass)44.5:factor(reg_name)Grand Est                  0.731724
## time:factor(ageClass)54.5:factor(reg_name)Grand Est                  0.127468
## time:factor(ageClass)64.5:factor(reg_name)Grand Est                  0.314515
## time:factor(ageClass)74.5:factor(reg_name)Grand Est                  0.939533
## time:factor(ageClass)84.5:factor(reg_name)Grand Est                  0.003083
## time:factor(ageClass)94.5:factor(reg_name)Grand Est                  0.094753
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe                 0.980258
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe                 0.980252
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe                 0.980353
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe                 0.980064
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe                 0.980090
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe                 0.980297
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe                 0.979789
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe                 0.982112
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe                       NA
## time:factor(ageClass)14.5:factor(reg_name)Guyane                     0.999898
## time:factor(ageClass)24.5:factor(reg_name)Guyane                     0.999552
## time:factor(ageClass)34.5:factor(reg_name)Guyane                     0.976207
## time:factor(ageClass)44.5:factor(reg_name)Guyane                     0.999721
## time:factor(ageClass)54.5:factor(reg_name)Guyane                     0.998976
## time:factor(ageClass)64.5:factor(reg_name)Guyane                     0.999985
## time:factor(ageClass)74.5:factor(reg_name)Guyane                           NA
## time:factor(ageClass)84.5:factor(reg_name)Guyane                     0.999998
## time:factor(ageClass)94.5:factor(reg_name)Guyane                           NA
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France            3.24e-09
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France            0.138138
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France            0.915620
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France            0.572848
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France            0.429055
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France            0.045694
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France            0.034445
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France            0.834904
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France            0.038036
## time:factor(ageClass)14.5:factor(reg_name)Île-de-France              0.191452
## time:factor(ageClass)24.5:factor(reg_name)Île-de-France              0.035519
## time:factor(ageClass)34.5:factor(reg_name)Île-de-France              0.345912
## time:factor(ageClass)44.5:factor(reg_name)Île-de-France              0.230374
## time:factor(ageClass)54.5:factor(reg_name)Île-de-France              0.216395
## time:factor(ageClass)64.5:factor(reg_name)Île-de-France              0.031747
## time:factor(ageClass)74.5:factor(reg_name)Île-de-France              0.920835
## time:factor(ageClass)84.5:factor(reg_name)Île-de-France              1.58e-09
## time:factor(ageClass)94.5:factor(reg_name)Île-de-France              0.000474
## time:factor(ageClass)14.5:factor(reg_name)La Réunion                 0.074557
## time:factor(ageClass)24.5:factor(reg_name)La Réunion                 0.089454
## time:factor(ageClass)34.5:factor(reg_name)La Réunion                 0.005890
## time:factor(ageClass)44.5:factor(reg_name)La Réunion                 0.005010
## time:factor(ageClass)54.5:factor(reg_name)La Réunion                 0.006686
## time:factor(ageClass)64.5:factor(reg_name)La Réunion                 6.14e-07
## time:factor(ageClass)74.5:factor(reg_name)La Réunion                 0.000363
## time:factor(ageClass)84.5:factor(reg_name)La Réunion                 0.999485
## time:factor(ageClass)94.5:factor(reg_name)La Réunion                       NA
## time:factor(ageClass)14.5:factor(reg_name)Martinique                 0.315998
## time:factor(ageClass)24.5:factor(reg_name)Martinique                 0.115686
## time:factor(ageClass)34.5:factor(reg_name)Martinique                 0.068050
## time:factor(ageClass)44.5:factor(reg_name)Martinique                 0.711263
## time:factor(ageClass)54.5:factor(reg_name)Martinique                 0.054168
## time:factor(ageClass)64.5:factor(reg_name)Martinique                 0.114524
## time:factor(ageClass)74.5:factor(reg_name)Martinique                 0.003144
## time:factor(ageClass)84.5:factor(reg_name)Martinique                 0.088548
## time:factor(ageClass)94.5:factor(reg_name)Martinique                 0.262260
## time:factor(ageClass)14.5:factor(reg_name)Mayotte                    0.999927
## time:factor(ageClass)24.5:factor(reg_name)Mayotte                    0.999918
## time:factor(ageClass)34.5:factor(reg_name)Mayotte                    0.999960
## time:factor(ageClass)44.5:factor(reg_name)Mayotte                    0.999944
## time:factor(ageClass)54.5:factor(reg_name)Mayotte                    0.999918
## time:factor(ageClass)64.5:factor(reg_name)Mayotte                    0.999986
## time:factor(ageClass)74.5:factor(reg_name)Mayotte                    0.999970
## time:factor(ageClass)84.5:factor(reg_name)Mayotte                          NA
## time:factor(ageClass)94.5:factor(reg_name)Mayotte                          NA
## time:factor(ageClass)14.5:factor(reg_name)Normandie                  0.000543
## time:factor(ageClass)24.5:factor(reg_name)Normandie                  0.127555
## time:factor(ageClass)34.5:factor(reg_name)Normandie                  6.96e-06
## time:factor(ageClass)44.5:factor(reg_name)Normandie                  0.112447
## time:factor(ageClass)54.5:factor(reg_name)Normandie                  0.270554
## time:factor(ageClass)64.5:factor(reg_name)Normandie                  0.032705
## time:factor(ageClass)74.5:factor(reg_name)Normandie                  0.192578
## time:factor(ageClass)84.5:factor(reg_name)Normandie                  0.000126
## time:factor(ageClass)94.5:factor(reg_name)Normandie                  0.000171
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine         1.15e-06
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine         2.16e-05
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine         0.000705
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine         0.024018
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine         1.00e-05
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine         0.980549
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine         0.027052
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine         2.37e-05
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine         0.002071
## time:factor(ageClass)14.5:factor(reg_name)Occitanie                  0.250787
## time:factor(ageClass)24.5:factor(reg_name)Occitanie                  0.174923
## time:factor(ageClass)34.5:factor(reg_name)Occitanie                  0.162450
## time:factor(ageClass)44.5:factor(reg_name)Occitanie                  0.181427
## time:factor(ageClass)54.5:factor(reg_name)Occitanie                  0.893862
## time:factor(ageClass)64.5:factor(reg_name)Occitanie                  0.013858
## time:factor(ageClass)74.5:factor(reg_name)Occitanie                  0.028781
## time:factor(ageClass)84.5:factor(reg_name)Occitanie                  0.303292
## time:factor(ageClass)94.5:factor(reg_name)Occitanie                  0.000860
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire           0.206675
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire           0.230262
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire           0.973139
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire           0.059835
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire           0.164168
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire           0.001355
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire           0.076351
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire           0.012728
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire           0.000336
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.000170
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.209481
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.954076
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.138076
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.209210
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.475071
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.004734
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur 2.25e-06
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur 0.000361
##                                                                         
## (Intercept)                                                          ***
## time                                                                 ***
## factor(ageClass)14.5                                                    
## factor(ageClass)24.5                                                 ***
## factor(ageClass)34.5                                                 ***
## factor(ageClass)44.5                                                 ***
## factor(ageClass)54.5                                                 ***
## factor(ageClass)64.5                                                 ***
## factor(ageClass)74.5                                                 ***
## factor(ageClass)84.5                                                 ***
## factor(ageClass)94.5                                                 ***
## factor(reg_name)Bourgogne-Franche-Comté                              ***
## factor(reg_name)Bretagne                                             ***
## factor(reg_name)Centre-Val de Loire                                     
## factor(reg_name)Corse                                                ***
## factor(reg_name)Grand Est                                            ***
## factor(reg_name)Guadeloupe                                              
## factor(reg_name)Guyane                                                  
## factor(reg_name)Hauts-de-France                                      ***
## factor(reg_name)Île-de-France                                        ***
## factor(reg_name)La Réunion                                           ***
## factor(reg_name)Martinique                                           .  
## factor(reg_name)Mayotte                                                 
## factor(reg_name)Normandie                                               
## factor(reg_name)Nouvelle-Aquitaine                                   ** 
## factor(reg_name)Occitanie                                            ***
## factor(reg_name)Pays de la Loire                                     ** 
## factor(reg_name)Provence-Alpes-Côte d'Azur                           ***
## time:factor(ageClass)14.5                                            ** 
## time:factor(ageClass)24.5                                               
## time:factor(ageClass)34.5                                               
## time:factor(ageClass)44.5                                               
## time:factor(ageClass)54.5                                            .  
## time:factor(ageClass)64.5                                            ***
## time:factor(ageClass)74.5                                            ***
## time:factor(ageClass)84.5                                               
## time:factor(ageClass)94.5                                               
## time:factor(reg_name)Bourgogne-Franche-Comté                            
## time:factor(reg_name)Bretagne                                        *  
## time:factor(reg_name)Centre-Val de Loire                                
## time:factor(reg_name)Corse                                           ***
## time:factor(reg_name)Grand Est                                          
## time:factor(reg_name)Guadeloupe                                         
## time:factor(reg_name)Guyane                                             
## time:factor(reg_name)Hauts-de-France                                 ** 
## time:factor(reg_name)Île-de-France                                   ***
## time:factor(reg_name)La Réunion                                         
## time:factor(reg_name)Martinique                                         
## time:factor(reg_name)Mayotte                                            
## time:factor(reg_name)Normandie                                          
## time:factor(reg_name)Nouvelle-Aquitaine                              ** 
## time:factor(reg_name)Occitanie                                          
## time:factor(reg_name)Pays de la Loire                                   
## time:factor(reg_name)Provence-Alpes-Côte d'Azur                         
## factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté         .  
## factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté         .  
## factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté            
## factor(ageClass)14.5:factor(reg_name)Bretagne                        .  
## factor(ageClass)24.5:factor(reg_name)Bretagne                        ** 
## factor(ageClass)34.5:factor(reg_name)Bretagne                        .  
## factor(ageClass)44.5:factor(reg_name)Bretagne                           
## factor(ageClass)54.5:factor(reg_name)Bretagne                           
## factor(ageClass)64.5:factor(reg_name)Bretagne                           
## factor(ageClass)74.5:factor(reg_name)Bretagne                           
## factor(ageClass)84.5:factor(reg_name)Bretagne                           
## factor(ageClass)94.5:factor(reg_name)Bretagne                           
## factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire             .  
## factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire             *  
## factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire                
## factor(ageClass)14.5:factor(reg_name)Corse                           ***
## factor(ageClass)24.5:factor(reg_name)Corse                           ***
## factor(ageClass)34.5:factor(reg_name)Corse                           ***
## factor(ageClass)44.5:factor(reg_name)Corse                           ** 
## factor(ageClass)54.5:factor(reg_name)Corse                           *  
## factor(ageClass)64.5:factor(reg_name)Corse                           ** 
## factor(ageClass)74.5:factor(reg_name)Corse                           ** 
## factor(ageClass)84.5:factor(reg_name)Corse                              
## factor(ageClass)94.5:factor(reg_name)Corse                           *  
## factor(ageClass)14.5:factor(reg_name)Grand Est                       ***
## factor(ageClass)24.5:factor(reg_name)Grand Est                       ** 
## factor(ageClass)34.5:factor(reg_name)Grand Est                       *  
## factor(ageClass)44.5:factor(reg_name)Grand Est                       ** 
## factor(ageClass)54.5:factor(reg_name)Grand Est                       ***
## factor(ageClass)64.5:factor(reg_name)Grand Est                       ***
## factor(ageClass)74.5:factor(reg_name)Grand Est                       *  
## factor(ageClass)84.5:factor(reg_name)Grand Est                       *  
## factor(ageClass)94.5:factor(reg_name)Grand Est                       ** 
## factor(ageClass)14.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)24.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)34.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)44.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)54.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)64.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)74.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)84.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)94.5:factor(reg_name)Guadeloupe                         
## factor(ageClass)14.5:factor(reg_name)Guyane                             
## factor(ageClass)24.5:factor(reg_name)Guyane                             
## factor(ageClass)34.5:factor(reg_name)Guyane                             
## factor(ageClass)44.5:factor(reg_name)Guyane                             
## factor(ageClass)54.5:factor(reg_name)Guyane                             
## factor(ageClass)64.5:factor(reg_name)Guyane                             
## factor(ageClass)74.5:factor(reg_name)Guyane                             
## factor(ageClass)84.5:factor(reg_name)Guyane                             
## factor(ageClass)94.5:factor(reg_name)Guyane                             
## factor(ageClass)14.5:factor(reg_name)Hauts-de-France                 ** 
## factor(ageClass)24.5:factor(reg_name)Hauts-de-France                    
## factor(ageClass)34.5:factor(reg_name)Hauts-de-France                    
## factor(ageClass)44.5:factor(reg_name)Hauts-de-France                    
## factor(ageClass)54.5:factor(reg_name)Hauts-de-France                 *  
## factor(ageClass)64.5:factor(reg_name)Hauts-de-France                 ***
## factor(ageClass)74.5:factor(reg_name)Hauts-de-France                 ***
## factor(ageClass)84.5:factor(reg_name)Hauts-de-France                 ***
## factor(ageClass)94.5:factor(reg_name)Hauts-de-France                 ***
## factor(ageClass)14.5:factor(reg_name)Île-de-France                      
## factor(ageClass)24.5:factor(reg_name)Île-de-France                      
## factor(ageClass)34.5:factor(reg_name)Île-de-France                      
## factor(ageClass)44.5:factor(reg_name)Île-de-France                   *  
## factor(ageClass)54.5:factor(reg_name)Île-de-France                   *  
## factor(ageClass)64.5:factor(reg_name)Île-de-France                   ***
## factor(ageClass)74.5:factor(reg_name)Île-de-France                      
## factor(ageClass)84.5:factor(reg_name)Île-de-France                   ***
## factor(ageClass)94.5:factor(reg_name)Île-de-France                      
## factor(ageClass)14.5:factor(reg_name)La Réunion                      *  
## factor(ageClass)24.5:factor(reg_name)La Réunion                      *  
## factor(ageClass)34.5:factor(reg_name)La Réunion                      ** 
## factor(ageClass)44.5:factor(reg_name)La Réunion                      ** 
## factor(ageClass)54.5:factor(reg_name)La Réunion                      ** 
## factor(ageClass)64.5:factor(reg_name)La Réunion                      ***
## factor(ageClass)74.5:factor(reg_name)La Réunion                      ***
## factor(ageClass)84.5:factor(reg_name)La Réunion                         
## factor(ageClass)94.5:factor(reg_name)La Réunion                         
## factor(ageClass)14.5:factor(reg_name)Martinique                         
## factor(ageClass)24.5:factor(reg_name)Martinique                      *  
## factor(ageClass)34.5:factor(reg_name)Martinique                      *  
## factor(ageClass)44.5:factor(reg_name)Martinique                         
## factor(ageClass)54.5:factor(reg_name)Martinique                      *  
## factor(ageClass)64.5:factor(reg_name)Martinique                      .  
## factor(ageClass)74.5:factor(reg_name)Martinique                      ** 
## factor(ageClass)84.5:factor(reg_name)Martinique                         
## factor(ageClass)94.5:factor(reg_name)Martinique                         
## factor(ageClass)14.5:factor(reg_name)Mayotte                            
## factor(ageClass)24.5:factor(reg_name)Mayotte                            
## factor(ageClass)34.5:factor(reg_name)Mayotte                            
## factor(ageClass)44.5:factor(reg_name)Mayotte                            
## factor(ageClass)54.5:factor(reg_name)Mayotte                            
## factor(ageClass)64.5:factor(reg_name)Mayotte                            
## factor(ageClass)74.5:factor(reg_name)Mayotte                            
## factor(ageClass)84.5:factor(reg_name)Mayotte                            
## factor(ageClass)94.5:factor(reg_name)Mayotte                            
## factor(ageClass)14.5:factor(reg_name)Normandie                          
## factor(ageClass)24.5:factor(reg_name)Normandie                          
## factor(ageClass)34.5:factor(reg_name)Normandie                       *  
## factor(ageClass)44.5:factor(reg_name)Normandie                       *  
## factor(ageClass)54.5:factor(reg_name)Normandie                       .  
## factor(ageClass)64.5:factor(reg_name)Normandie                       ***
## factor(ageClass)74.5:factor(reg_name)Normandie                          
## factor(ageClass)84.5:factor(reg_name)Normandie                          
## factor(ageClass)94.5:factor(reg_name)Normandie                          
## factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine              *  
## factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine              ** 
## factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine              ***
## factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine                 
## factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine              ***
## factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine                 
## factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine              ***
## factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine              ***
## factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine              ***
## factor(ageClass)14.5:factor(reg_name)Occitanie                          
## factor(ageClass)24.5:factor(reg_name)Occitanie                          
## factor(ageClass)34.5:factor(reg_name)Occitanie                          
## factor(ageClass)44.5:factor(reg_name)Occitanie                          
## factor(ageClass)54.5:factor(reg_name)Occitanie                          
## factor(ageClass)64.5:factor(reg_name)Occitanie                          
## factor(ageClass)74.5:factor(reg_name)Occitanie                          
## factor(ageClass)84.5:factor(reg_name)Occitanie                       ** 
## factor(ageClass)94.5:factor(reg_name)Occitanie                       ***
## factor(ageClass)14.5:factor(reg_name)Pays de la Loire                   
## factor(ageClass)24.5:factor(reg_name)Pays de la Loire                   
## factor(ageClass)34.5:factor(reg_name)Pays de la Loire                   
## factor(ageClass)44.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)54.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)64.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)74.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)84.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)94.5:factor(reg_name)Pays de la Loire                ***
## factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur      ***
## factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur      *  
## factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur         
## factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur      *  
## factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur         
## factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur      .  
## factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur      ***
## factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur      *  
## factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur      *  
## time:factor(ageClass)14.5:factor(reg_name)Bourgogne-Franche-Comté    *  
## time:factor(ageClass)24.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)34.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)44.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)54.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)64.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)74.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)84.5:factor(reg_name)Bourgogne-Franche-Comté       
## time:factor(ageClass)94.5:factor(reg_name)Bourgogne-Franche-Comté    .  
## time:factor(ageClass)14.5:factor(reg_name)Bretagne                   *  
## time:factor(ageClass)24.5:factor(reg_name)Bretagne                   ***
## time:factor(ageClass)34.5:factor(reg_name)Bretagne                      
## time:factor(ageClass)44.5:factor(reg_name)Bretagne                      
## time:factor(ageClass)54.5:factor(reg_name)Bretagne                      
## time:factor(ageClass)64.5:factor(reg_name)Bretagne                      
## time:factor(ageClass)74.5:factor(reg_name)Bretagne                      
## time:factor(ageClass)84.5:factor(reg_name)Bretagne                   ***
## time:factor(ageClass)94.5:factor(reg_name)Bretagne                   ** 
## time:factor(ageClass)14.5:factor(reg_name)Centre-Val de Loire           
## time:factor(ageClass)24.5:factor(reg_name)Centre-Val de Loire        *  
## time:factor(ageClass)34.5:factor(reg_name)Centre-Val de Loire        ** 
## time:factor(ageClass)44.5:factor(reg_name)Centre-Val de Loire        *  
## time:factor(ageClass)54.5:factor(reg_name)Centre-Val de Loire        .  
## time:factor(ageClass)64.5:factor(reg_name)Centre-Val de Loire        ** 
## time:factor(ageClass)74.5:factor(reg_name)Centre-Val de Loire           
## time:factor(ageClass)84.5:factor(reg_name)Centre-Val de Loire           
## time:factor(ageClass)94.5:factor(reg_name)Centre-Val de Loire           
## time:factor(ageClass)14.5:factor(reg_name)Corse                      ***
## time:factor(ageClass)24.5:factor(reg_name)Corse                      ***
## time:factor(ageClass)34.5:factor(reg_name)Corse                      ***
## time:factor(ageClass)44.5:factor(reg_name)Corse                      *  
## time:factor(ageClass)54.5:factor(reg_name)Corse                      ** 
## time:factor(ageClass)64.5:factor(reg_name)Corse                      ***
## time:factor(ageClass)74.5:factor(reg_name)Corse                      ***
## time:factor(ageClass)84.5:factor(reg_name)Corse                      .  
## time:factor(ageClass)94.5:factor(reg_name)Corse                         
## time:factor(ageClass)14.5:factor(reg_name)Grand Est                  ***
## time:factor(ageClass)24.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)34.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)44.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)54.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)64.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)74.5:factor(reg_name)Grand Est                     
## time:factor(ageClass)84.5:factor(reg_name)Grand Est                  ** 
## time:factor(ageClass)94.5:factor(reg_name)Grand Est                  .  
## time:factor(ageClass)14.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)24.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)34.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)44.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)54.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)64.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)74.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)84.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)94.5:factor(reg_name)Guadeloupe                    
## time:factor(ageClass)14.5:factor(reg_name)Guyane                        
## time:factor(ageClass)24.5:factor(reg_name)Guyane                        
## time:factor(ageClass)34.5:factor(reg_name)Guyane                        
## time:factor(ageClass)44.5:factor(reg_name)Guyane                        
## time:factor(ageClass)54.5:factor(reg_name)Guyane                        
## time:factor(ageClass)64.5:factor(reg_name)Guyane                        
## time:factor(ageClass)74.5:factor(reg_name)Guyane                        
## time:factor(ageClass)84.5:factor(reg_name)Guyane                        
## time:factor(ageClass)94.5:factor(reg_name)Guyane                        
## time:factor(ageClass)14.5:factor(reg_name)Hauts-de-France            ***
## time:factor(ageClass)24.5:factor(reg_name)Hauts-de-France               
## time:factor(ageClass)34.5:factor(reg_name)Hauts-de-France               
## time:factor(ageClass)44.5:factor(reg_name)Hauts-de-France               
## time:factor(ageClass)54.5:factor(reg_name)Hauts-de-France               
## time:factor(ageClass)64.5:factor(reg_name)Hauts-de-France            *  
## time:factor(ageClass)74.5:factor(reg_name)Hauts-de-France            *  
## time:factor(ageClass)84.5:factor(reg_name)Hauts-de-France               
## time:factor(ageClass)94.5:factor(reg_name)Hauts-de-France            *  
## time:factor(ageClass)14.5:factor(reg_name)Île-de-France                 
## time:factor(ageClass)24.5:factor(reg_name)Île-de-France              *  
## time:factor(ageClass)34.5:factor(reg_name)Île-de-France                 
## time:factor(ageClass)44.5:factor(reg_name)Île-de-France                 
## time:factor(ageClass)54.5:factor(reg_name)Île-de-France                 
## time:factor(ageClass)64.5:factor(reg_name)Île-de-France              *  
## time:factor(ageClass)74.5:factor(reg_name)Île-de-France                 
## time:factor(ageClass)84.5:factor(reg_name)Île-de-France              ***
## time:factor(ageClass)94.5:factor(reg_name)Île-de-France              ***
## time:factor(ageClass)14.5:factor(reg_name)La Réunion                 .  
## time:factor(ageClass)24.5:factor(reg_name)La Réunion                 .  
## time:factor(ageClass)34.5:factor(reg_name)La Réunion                 ** 
## time:factor(ageClass)44.5:factor(reg_name)La Réunion                 ** 
## time:factor(ageClass)54.5:factor(reg_name)La Réunion                 ** 
## time:factor(ageClass)64.5:factor(reg_name)La Réunion                 ***
## time:factor(ageClass)74.5:factor(reg_name)La Réunion                 ***
## time:factor(ageClass)84.5:factor(reg_name)La Réunion                    
## time:factor(ageClass)94.5:factor(reg_name)La Réunion                    
## time:factor(ageClass)14.5:factor(reg_name)Martinique                    
## time:factor(ageClass)24.5:factor(reg_name)Martinique                    
## time:factor(ageClass)34.5:factor(reg_name)Martinique                 .  
## time:factor(ageClass)44.5:factor(reg_name)Martinique                    
## time:factor(ageClass)54.5:factor(reg_name)Martinique                 .  
## time:factor(ageClass)64.5:factor(reg_name)Martinique                    
## time:factor(ageClass)74.5:factor(reg_name)Martinique                 ** 
## time:factor(ageClass)84.5:factor(reg_name)Martinique                 .  
## time:factor(ageClass)94.5:factor(reg_name)Martinique                    
## time:factor(ageClass)14.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)24.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)34.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)44.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)54.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)64.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)74.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)84.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)94.5:factor(reg_name)Mayotte                       
## time:factor(ageClass)14.5:factor(reg_name)Normandie                  ***
## time:factor(ageClass)24.5:factor(reg_name)Normandie                     
## time:factor(ageClass)34.5:factor(reg_name)Normandie                  ***
## time:factor(ageClass)44.5:factor(reg_name)Normandie                     
## time:factor(ageClass)54.5:factor(reg_name)Normandie                     
## time:factor(ageClass)64.5:factor(reg_name)Normandie                  *  
## time:factor(ageClass)74.5:factor(reg_name)Normandie                     
## time:factor(ageClass)84.5:factor(reg_name)Normandie                  ***
## time:factor(ageClass)94.5:factor(reg_name)Normandie                  ***
## time:factor(ageClass)14.5:factor(reg_name)Nouvelle-Aquitaine         ***
## time:factor(ageClass)24.5:factor(reg_name)Nouvelle-Aquitaine         ***
## time:factor(ageClass)34.5:factor(reg_name)Nouvelle-Aquitaine         ***
## time:factor(ageClass)44.5:factor(reg_name)Nouvelle-Aquitaine         *  
## time:factor(ageClass)54.5:factor(reg_name)Nouvelle-Aquitaine         ***
## time:factor(ageClass)64.5:factor(reg_name)Nouvelle-Aquitaine            
## time:factor(ageClass)74.5:factor(reg_name)Nouvelle-Aquitaine         *  
## time:factor(ageClass)84.5:factor(reg_name)Nouvelle-Aquitaine         ***
## time:factor(ageClass)94.5:factor(reg_name)Nouvelle-Aquitaine         ** 
## time:factor(ageClass)14.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)24.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)34.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)44.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)54.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)64.5:factor(reg_name)Occitanie                  *  
## time:factor(ageClass)74.5:factor(reg_name)Occitanie                  *  
## time:factor(ageClass)84.5:factor(reg_name)Occitanie                     
## time:factor(ageClass)94.5:factor(reg_name)Occitanie                  ***
## time:factor(ageClass)14.5:factor(reg_name)Pays de la Loire              
## time:factor(ageClass)24.5:factor(reg_name)Pays de la Loire              
## time:factor(ageClass)34.5:factor(reg_name)Pays de la Loire              
## time:factor(ageClass)44.5:factor(reg_name)Pays de la Loire           .  
## time:factor(ageClass)54.5:factor(reg_name)Pays de la Loire              
## time:factor(ageClass)64.5:factor(reg_name)Pays de la Loire           ** 
## time:factor(ageClass)74.5:factor(reg_name)Pays de la Loire           .  
## time:factor(ageClass)84.5:factor(reg_name)Pays de la Loire           *  
## time:factor(ageClass)94.5:factor(reg_name)Pays de la Loire           ***
## time:factor(ageClass)14.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## time:factor(ageClass)24.5:factor(reg_name)Provence-Alpes-Côte d'Azur    
## time:factor(ageClass)34.5:factor(reg_name)Provence-Alpes-Côte d'Azur    
## time:factor(ageClass)44.5:factor(reg_name)Provence-Alpes-Côte d'Azur    
## time:factor(ageClass)54.5:factor(reg_name)Provence-Alpes-Côte d'Azur    
## time:factor(ageClass)64.5:factor(reg_name)Provence-Alpes-Côte d'Azur    
## time:factor(ageClass)74.5:factor(reg_name)Provence-Alpes-Côte d'Azur ** 
## time:factor(ageClass)84.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## time:factor(ageClass)94.5:factor(reg_name)Provence-Alpes-Côte d'Azur ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   2246.2  on 2701  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 18927
## 
## Number of Fisher Scoring iterations: 17

# Without interaction
mdl1 <- glm(cbind(V1, notV1) ~ time*factor(reg_name) + factor(ageClass), data = dat.regions.ages, family = "binomial")
summary(mdl1)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(reg_name) + factor(ageClass), 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.5584  -0.7909   0.0000   0.8827   5.0948  
## 
## Coefficients:
##                                                   Estimate Std. Error z value
## (Intercept)                                     -2.947e-01  1.169e-02 -25.203
## time                                             5.735e-02  9.192e-04  62.386
## factor(reg_name)Bourgogne-Franche-Comté         -5.194e-01  1.936e-02 -26.825
## factor(reg_name)Bretagne                         5.714e-01  1.995e-02  28.634
## factor(reg_name)Centre-Val de Loire              9.113e-02  2.058e-02   4.428
## factor(reg_name)Corse                            1.130e+00  6.151e-02  18.370
## factor(reg_name)Grand Est                       -5.024e-01  1.493e-02 -33.651
## factor(reg_name)Guadeloupe                       9.994e-01  1.437e-01   6.954
## factor(reg_name)Guyane                          -9.876e-01  2.583e-01  -3.824
## factor(reg_name)Hauts-de-France                  5.846e-01  1.204e-02  48.561
## factor(reg_name)Île-de-France                    6.461e-01  1.109e-02  58.283
## factor(reg_name)La Réunion                      -1.960e+00  9.085e-02 -21.573
## factor(reg_name)Martinique                       4.160e-01  1.295e-01   3.213
## factor(reg_name)Mayotte                         -5.280e+00  4.552e-01 -11.601
## factor(reg_name)Normandie                       -3.531e-02  1.802e-02  -1.959
## factor(reg_name)Nouvelle-Aquitaine              -4.575e-02  1.681e-02  -2.722
## factor(reg_name)Occitanie                        3.266e-01  1.428e-02  22.881
## factor(reg_name)Pays de la Loire                 1.516e-02  1.675e-02   0.905
## factor(reg_name)Provence-Alpes-Côte d'Azur       3.144e-01  1.255e-02  25.055
## factor(ageClass)14.5                            -5.841e-02  8.685e-03  -6.725
## factor(ageClass)24.5                            -1.115e-01  8.548e-03 -13.042
## factor(ageClass)34.5                            -8.241e-02  8.554e-03  -9.634
## factor(ageClass)44.5                            -7.708e-02  8.543e-03  -9.023
## factor(ageClass)54.5                            -1.583e-01  8.609e-03 -18.393
## factor(ageClass)64.5                            -2.466e-01  9.005e-03 -27.389
## factor(ageClass)74.5                            -4.342e-01  9.722e-03 -44.662
## factor(ageClass)84.5                            -7.102e-01  1.056e-02 -67.231
## factor(ageClass)94.5                            -8.899e-01  1.322e-02 -67.296
## time:factor(reg_name)Bourgogne-Franche-Comté     9.398e-03  1.919e-03   4.898
## time:factor(reg_name)Bretagne                   -1.462e-03  2.071e-03  -0.706
## time:factor(reg_name)Centre-Val de Loire        -4.587e-06  2.014e-03  -0.002
## time:factor(reg_name)Corse                      -1.819e-02  6.189e-03  -2.940
## time:factor(reg_name)Grand Est                   2.785e-03  1.466e-03   1.900
## time:factor(reg_name)Guadeloupe                  5.792e-02  1.459e-02   3.970
## time:factor(reg_name)Guyane                      5.869e-02  2.767e-02   2.121
## time:factor(reg_name)Hauts-de-France            -1.037e-02  1.220e-03  -8.506
## time:factor(reg_name)Île-de-France              -2.095e-02  1.116e-03 -18.771
## time:factor(reg_name)La Réunion                 -7.881e-02  8.551e-03  -9.216
## time:factor(reg_name)Martinique                  1.169e-02  1.310e-02   0.893
## time:factor(reg_name)Mayotte                     2.725e-02  4.174e-02   0.653
## time:factor(reg_name)Normandie                   1.865e-02  1.800e-03  10.361
## time:factor(reg_name)Nouvelle-Aquitaine          6.240e-03  1.700e-03   3.669
## time:factor(reg_name)Occitanie                  -1.887e-03  1.456e-03  -1.296
## time:factor(reg_name)Pays de la Loire           -5.600e-03  1.683e-03  -3.327
## time:factor(reg_name)Provence-Alpes-Côte d'Azur  1.672e-02  1.302e-03  12.844
##                                                 Pr(>|z|)    
## (Intercept)                                      < 2e-16 ***
## time                                             < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté          < 2e-16 ***
## factor(reg_name)Bretagne                         < 2e-16 ***
## factor(reg_name)Centre-Val de Loire             9.50e-06 ***
## factor(reg_name)Corse                            < 2e-16 ***
## factor(reg_name)Grand Est                        < 2e-16 ***
## factor(reg_name)Guadeloupe                      3.55e-12 ***
## factor(reg_name)Guyane                          0.000131 ***
## factor(reg_name)Hauts-de-France                  < 2e-16 ***
## factor(reg_name)Île-de-France                    < 2e-16 ***
## factor(reg_name)La Réunion                       < 2e-16 ***
## factor(reg_name)Martinique                      0.001312 ** 
## factor(reg_name)Mayotte                          < 2e-16 ***
## factor(reg_name)Normandie                       0.050128 .  
## factor(reg_name)Nouvelle-Aquitaine              0.006491 ** 
## factor(reg_name)Occitanie                        < 2e-16 ***
## factor(reg_name)Pays de la Loire                0.365481    
## factor(reg_name)Provence-Alpes-Côte d'Azur       < 2e-16 ***
## factor(ageClass)14.5                            1.75e-11 ***
## factor(ageClass)24.5                             < 2e-16 ***
## factor(ageClass)34.5                             < 2e-16 ***
## factor(ageClass)44.5                             < 2e-16 ***
## factor(ageClass)54.5                             < 2e-16 ***
## factor(ageClass)64.5                             < 2e-16 ***
## factor(ageClass)74.5                             < 2e-16 ***
## factor(ageClass)84.5                             < 2e-16 ***
## factor(ageClass)94.5                             < 2e-16 ***
## time:factor(reg_name)Bourgogne-Franche-Comté    9.69e-07 ***
## time:factor(reg_name)Bretagne                   0.480353    
## time:factor(reg_name)Centre-Val de Loire        0.998183    
## time:factor(reg_name)Corse                      0.003286 ** 
## time:factor(reg_name)Grand Est                  0.057442 .  
## time:factor(reg_name)Guadeloupe                 7.19e-05 ***
## time:factor(reg_name)Guyane                     0.033920 *  
## time:factor(reg_name)Hauts-de-France             < 2e-16 ***
## time:factor(reg_name)Île-de-France               < 2e-16 ***
## time:factor(reg_name)La Réunion                  < 2e-16 ***
## time:factor(reg_name)Martinique                 0.371936    
## time:factor(reg_name)Mayotte                    0.513930    
## time:factor(reg_name)Normandie                   < 2e-16 ***
## time:factor(reg_name)Nouvelle-Aquitaine         0.000243 ***
## time:factor(reg_name)Occitanie                  0.194864    
## time:factor(reg_name)Pays de la Loire           0.000877 ***
## time:factor(reg_name)Provence-Alpes-Côte d'Azur  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   6054.6  on 3005  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 22128
## 
## Number of Fisher Scoring iterations: 6

# Without interaction
mdl1bis <- glm(cbind(V1, notV1) ~ time*factor(ageClass) + factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl1bis)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * factor(ageClass) + factor(reg_name), 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.0968  -0.9147   0.0000   0.9812   7.4498  
## 
## Coefficients:
##                                             Estimate Std. Error z value
## (Intercept)                                -0.170794   0.015381 -11.105
## time                                        0.042839   0.001475  29.041
## factor(ageClass)14.5                       -0.127467   0.017022  -7.488
## factor(ageClass)24.5                       -0.214189   0.016773 -12.770
## factor(ageClass)34.5                       -0.145865   0.016735  -8.716
## factor(ageClass)44.5                       -0.143081   0.016709  -8.563
## factor(ageClass)54.5                       -0.251776   0.016875 -14.920
## factor(ageClass)64.5                       -0.340223   0.017704 -19.217
## factor(ageClass)74.5                       -0.650177   0.019228 -33.814
## factor(ageClass)84.5                       -0.918696   0.020638 -44.515
## factor(ageClass)94.5                       -1.053709   0.025276 -41.688
## factor(reg_name)Bourgogne-Franche-Comté    -0.435910   0.009565 -45.572
## factor(reg_name)Bretagne                    0.557710   0.010378  53.740
## factor(reg_name)Centre-Val de Loire         0.091897   0.010157   9.047
## factor(reg_name)Corse                       0.973375   0.031223  31.175
## factor(reg_name)Grand Est                  -0.475638   0.007314 -65.028
## factor(reg_name)Guadeloupe                  1.524675   0.068491  22.261
## factor(reg_name)Guyane                     -0.535538   0.133505  -4.011
## factor(reg_name)Hauts-de-France             0.495943   0.006125  80.966
## factor(reg_name)Île-de-France               0.465823   0.005624  82.834
## factor(reg_name)La Réunion                 -2.754360   0.042107 -65.413
## factor(reg_name)Martinique                  0.518608   0.061566   8.424
## factor(reg_name)Mayotte                    -5.022954   0.204737 -24.534
## factor(reg_name)Normandie                   0.127488   0.008934  14.270
## factor(reg_name)Nouvelle-Aquitaine          0.007811   0.008468   0.922
## factor(reg_name)Occitanie                   0.311201   0.007375  42.199
## factor(reg_name)Pays de la Loire           -0.032831   0.008538  -3.845
## factor(reg_name)Provence-Alpes-Côte d'Azur  0.446784   0.006487  68.876
## time:factor(ageClass)14.5                   0.008044   0.001702   4.727
## time:factor(ageClass)24.5                   0.012047   0.001677   7.186
## time:factor(ageClass)34.5                   0.007343   0.001676   4.381
## time:factor(ageClass)44.5                   0.007737   0.001675   4.618
## time:factor(ageClass)54.5                   0.011021   0.001691   6.518
## time:factor(ageClass)64.5                   0.011005   0.001769   6.220
## time:factor(ageClass)74.5                   0.025182   0.001923  13.097
## time:factor(ageClass)84.5                   0.024747   0.002089  11.846
## time:factor(ageClass)94.5                   0.019538   0.002628   7.433
##                                            Pr(>|z|)    
## (Intercept)                                 < 2e-16 ***
## time                                        < 2e-16 ***
## factor(ageClass)14.5                       6.98e-14 ***
## factor(ageClass)24.5                        < 2e-16 ***
## factor(ageClass)34.5                        < 2e-16 ***
## factor(ageClass)44.5                        < 2e-16 ***
## factor(ageClass)54.5                        < 2e-16 ***
## factor(ageClass)64.5                        < 2e-16 ***
## factor(ageClass)74.5                        < 2e-16 ***
## factor(ageClass)84.5                        < 2e-16 ***
## factor(ageClass)94.5                        < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté     < 2e-16 ***
## factor(reg_name)Bretagne                    < 2e-16 ***
## factor(reg_name)Centre-Val de Loire         < 2e-16 ***
## factor(reg_name)Corse                       < 2e-16 ***
## factor(reg_name)Grand Est                   < 2e-16 ***
## factor(reg_name)Guadeloupe                  < 2e-16 ***
## factor(reg_name)Guyane                     6.04e-05 ***
## factor(reg_name)Hauts-de-France             < 2e-16 ***
## factor(reg_name)Île-de-France               < 2e-16 ***
## factor(reg_name)La Réunion                  < 2e-16 ***
## factor(reg_name)Martinique                  < 2e-16 ***
## factor(reg_name)Mayotte                     < 2e-16 ***
## factor(reg_name)Normandie                   < 2e-16 ***
## factor(reg_name)Nouvelle-Aquitaine          0.35635    
## factor(reg_name)Occitanie                   < 2e-16 ***
## factor(reg_name)Pays de la Loire            0.00012 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur  < 2e-16 ***
## time:factor(ageClass)14.5                  2.27e-06 ***
## time:factor(ageClass)24.5                  6.69e-13 ***
## time:factor(ageClass)34.5                  1.18e-05 ***
## time:factor(ageClass)44.5                  3.87e-06 ***
## time:factor(ageClass)54.5                  7.13e-11 ***
## time:factor(ageClass)64.5                  4.97e-10 ***
## time:factor(ageClass)74.5                   < 2e-16 ***
## time:factor(ageClass)84.5                   < 2e-16 ***
## time:factor(ageClass)94.5                  1.06e-13 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   7502.1  on 3013  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 23559
## 
## Number of Fisher Scoring iterations: 5

# Without interaction at all
mdl2 <- glm(cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl2)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name), 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -7.2722  -0.8808   0.0000   0.9799   8.0354  
## 
## Coefficients:
##                                              Estimate Std. Error z value
## (Intercept)                                -0.2648359  0.0090584 -29.236
## time                                        0.0537605  0.0003101 173.364
## factor(ageClass)14.5                       -0.0583640  0.0086809  -6.723
## factor(ageClass)24.5                       -0.1106522  0.0085445 -12.950
## factor(ageClass)34.5                       -0.0823989  0.0085504  -9.637
## factor(ageClass)44.5                       -0.0761394  0.0085391  -8.917
## factor(ageClass)54.5                       -0.1570956  0.0086044 -18.258
## factor(ageClass)64.5                       -0.2456723  0.0089999 -27.297
## factor(ageClass)74.5                       -0.4330799  0.0097156 -44.576
## factor(ageClass)84.5                       -0.7096711  0.0105554 -67.233
## factor(ageClass)94.5                       -0.8911538  0.0132095 -67.463
## factor(reg_name)Bourgogne-Franche-Comté    -0.4356291  0.0095640 -45.549
## factor(reg_name)Bretagne                    0.5582156  0.0103751  53.803
## factor(reg_name)Centre-Val de Loire         0.0927682  0.0101556   9.135
## factor(reg_name)Corse                       0.9752876  0.0312132  31.246
## factor(reg_name)Grand Est                  -0.4750509  0.0073146 -64.945
## factor(reg_name)Guadeloupe                  1.5243190  0.0684935  22.255
## factor(reg_name)Guyane                     -0.5351203  0.1335890  -4.006
## factor(reg_name)Hauts-de-France             0.4966018  0.0061247  81.082
## factor(reg_name)Île-de-France               0.4659388  0.0056232  82.860
## factor(reg_name)La Réunion                 -2.7567557  0.0421142 -65.459
## factor(reg_name)Martinique                  0.5188033  0.0615424   8.430
## factor(reg_name)Mayotte                    -5.0225215  0.2047367 -24.532
## factor(reg_name)Normandie                   0.1288819  0.0089326  14.428
## factor(reg_name)Nouvelle-Aquitaine          0.0076666  0.0084674   0.905
## factor(reg_name)Occitanie                   0.3102706  0.0073722  42.086
## factor(reg_name)Pays de la Loire           -0.0326336  0.0085370  -3.823
## factor(reg_name)Provence-Alpes-Côte d'Azur  0.4467034  0.0064850  68.883
##                                            Pr(>|z|)    
## (Intercept)                                 < 2e-16 ***
## time                                        < 2e-16 ***
## factor(ageClass)14.5                       1.78e-11 ***
## factor(ageClass)24.5                        < 2e-16 ***
## factor(ageClass)34.5                        < 2e-16 ***
## factor(ageClass)44.5                        < 2e-16 ***
## factor(ageClass)54.5                        < 2e-16 ***
## factor(ageClass)64.5                        < 2e-16 ***
## factor(ageClass)74.5                        < 2e-16 ***
## factor(ageClass)84.5                        < 2e-16 ***
## factor(ageClass)94.5                        < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté     < 2e-16 ***
## factor(reg_name)Bretagne                    < 2e-16 ***
## factor(reg_name)Centre-Val de Loire         < 2e-16 ***
## factor(reg_name)Corse                       < 2e-16 ***
## factor(reg_name)Grand Est                   < 2e-16 ***
## factor(reg_name)Guadeloupe                  < 2e-16 ***
## factor(reg_name)Guyane                     6.18e-05 ***
## factor(reg_name)Hauts-de-France             < 2e-16 ***
## factor(reg_name)Île-de-France               < 2e-16 ***
## factor(reg_name)La Réunion                  < 2e-16 ***
## factor(reg_name)Martinique                  < 2e-16 ***
## factor(reg_name)Mayotte                     < 2e-16 ***
## factor(reg_name)Normandie                   < 2e-16 ***
## factor(reg_name)Nouvelle-Aquitaine         0.365235    
## factor(reg_name)Occitanie                   < 2e-16 ***
## factor(reg_name)Pays de la Loire           0.000132 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   7844.6  on 3022  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 23884
## 
## Number of Fisher Scoring iterations: 5

## Likelihood ratio tests
anova(mdl1, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time * factor(reg_name) + factor(ageClass)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
##   Resid. Df Resid. Dev  Df Deviance  Pr(>Chi)    
## 1      3005     6054.6                           
## 2      2701     2246.2 304   3808.4 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

anova(mdl1bis, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time * factor(ageClass) + factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
##   Resid. Df Resid. Dev  Df Deviance  Pr(>Chi)    
## 1      3013     7502.1                           
## 2      2701     2246.2 312   5255.8 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

anova(mdl2, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time + factor(ageClass) + factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
##   Resid. Df Resid. Dev  Df Deviance  Pr(>Chi)    
## 1      3022     7844.6                           
## 2      2701     2246.2 321   5598.4 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

2. Age as quantitative

mdl3 <- glm(cbind(V1, notV1) ~ time * ageClass * factor(reg_name), data = dat.regions.ages, family = "binomial")
summary(mdl3)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ time * ageClass * factor(reg_name), 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -9.3444  -1.1485  -0.0175   0.8235   7.6969  
## 
## Coefficients:
##                                                            Estimate Std. Error
## (Intercept)                                               6.899e-03  1.937e-02
## time                                                      4.310e-02  1.961e-03
## ageClass                                                 -1.126e-02  4.034e-04
## factor(reg_name)Bourgogne-Franche-Comté                  -5.871e-01  4.152e-02
## factor(reg_name)Bretagne                                  3.933e-01  4.125e-02
## factor(reg_name)Centre-Val de Loire                       6.498e-02  4.448e-02
## factor(reg_name)Corse                                     4.198e-01  1.458e-01
## factor(reg_name)Grand Est                                -7.690e-01  3.106e-02
## factor(reg_name)Guadeloupe                                1.823e-01  3.723e-01
## factor(reg_name)Guyane                                   -1.799e+00  5.600e-01
## factor(reg_name)Hauts-de-France                           3.263e-01  2.569e-02
## factor(reg_name)Île-de-France                             5.480e-01  2.394e-02
## factor(reg_name)La Réunion                               -3.337e+00  2.179e-01
## factor(reg_name)Martinique                                9.231e-01  3.251e-01
## factor(reg_name)Mayotte                                  -1.494e+01  1.065e+01
## factor(reg_name)Normandie                                -1.743e-01  3.837e-02
## factor(reg_name)Nouvelle-Aquitaine                        7.943e-02  3.586e-02
## factor(reg_name)Occitanie                                 2.055e-01  3.067e-02
## factor(reg_name)Pays de la Loire                         -3.367e-01  3.518e-02
## factor(reg_name)Provence-Alpes-Côte d'Azur                3.529e-01  2.734e-02
## time:ageClass                                             3.390e-04  4.113e-05
## time:factor(reg_name)Bourgogne-Franche-Comté              1.083e-02  4.121e-03
## time:factor(reg_name)Bretagne                             1.518e-03  4.269e-03
## time:factor(reg_name)Centre-Val de Loire                 -4.705e-04  4.364e-03
## time:factor(reg_name)Corse                               -1.260e-03  1.412e-02
## time:factor(reg_name)Grand Est                            1.575e-02  3.080e-03
## time:factor(reg_name)Guadeloupe                           1.796e-01  3.950e-02
## time:factor(reg_name)Guyane                              -1.025e-01  6.655e-02
## time:factor(reg_name)Hauts-de-France                      7.519e-03  2.607e-03
## time:factor(reg_name)Île-de-France                       -2.028e-02  2.409e-03
## time:factor(reg_name)La Réunion                           3.157e-02  1.937e-02
## time:factor(reg_name)Martinique                          -2.597e-02  3.306e-02
## time:factor(reg_name)Mayotte                             -8.621e-01  1.114e+00
## time:factor(reg_name)Normandie                            2.664e-02  3.866e-03
## time:factor(reg_name)Nouvelle-Aquitaine                   9.780e-03  3.626e-03
## time:factor(reg_name)Occitanie                            1.077e-02  3.115e-03
## time:factor(reg_name)Pays de la Loire                     2.053e-02  3.532e-03
## time:factor(reg_name)Provence-Alpes-Côte d'Azur           1.161e-02  2.851e-03
## ageClass:factor(reg_name)Bourgogne-Franche-Comté          1.635e-03  8.394e-04
## ageClass:factor(reg_name)Bretagne                         3.954e-03  8.715e-04
## ageClass:factor(reg_name)Centre-Val de Loire              6.892e-04  8.860e-04
## ageClass:factor(reg_name)Corse                            1.605e-02  2.930e-03
## ageClass:factor(reg_name)Grand Est                        6.289e-03  6.565e-04
## ageClass:factor(reg_name)Guadeloupe                       1.925e-02  7.856e-03
## ageClass:factor(reg_name)Guyane                           1.802e-02  1.406e-02
## ageClass:factor(reg_name)Hauts-de-France                  6.174e-03  5.372e-04
## ageClass:factor(reg_name)Île-de-France                    2.469e-03  5.038e-04
## ageClass:factor(reg_name)La Réunion                       3.601e-02  4.814e-03
## ageClass:factor(reg_name)Martinique                      -1.002e-02  6.184e-03
## ageClass:factor(reg_name)Mayotte                          1.542e-01  1.638e-01
## ageClass:factor(reg_name)Normandie                        3.354e-03  7.927e-04
## ageClass:factor(reg_name)Nouvelle-Aquitaine              -2.962e-03  7.447e-04
## ageClass:factor(reg_name)Occitanie                        2.731e-03  6.160e-04
## ageClass:factor(reg_name)Pays de la Loire                 8.164e-03  7.280e-04
## ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur      -6.298e-04  5.549e-04
## time:ageClass:factor(reg_name)Bourgogne-Franche-Comté    -3.898e-05  8.417e-05
## time:ageClass:factor(reg_name)Bretagne                   -4.990e-05  9.166e-05
## time:ageClass:factor(reg_name)Centre-Val de Loire        -3.791e-06  8.731e-05
## time:ageClass:factor(reg_name)Corse                      -4.225e-04  2.865e-04
## time:ageClass:factor(reg_name)Grand Est                  -2.987e-04  6.509e-05
## time:ageClass:factor(reg_name)Guadeloupe                 -2.722e-03  7.998e-04
## time:ageClass:factor(reg_name)Guyane                      5.851e-03  1.867e-03
## time:ageClass:factor(reg_name)Hauts-de-France            -4.244e-04  5.474e-05
## time:ageClass:factor(reg_name)Île-de-France              -4.709e-06  5.108e-05
## time:ageClass:factor(reg_name)La Réunion                 -2.889e-03  4.523e-04
## time:ageClass:factor(reg_name)Martinique                  7.214e-04  6.154e-04
## time:ageClass:factor(reg_name)Mayotte                     1.309e-02  1.714e-02
## time:ageClass:factor(reg_name)Normandie                  -1.967e-04  7.929e-05
## time:ageClass:factor(reg_name)Nouvelle-Aquitaine         -8.710e-05  7.549e-05
## time:ageClass:factor(reg_name)Occitanie                  -2.941e-04  6.364e-05
## time:ageClass:factor(reg_name)Pays de la Loire           -6.167e-04  7.391e-05
## time:ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur  1.017e-04  5.817e-05
##                                                          z value Pr(>|z|)    
## (Intercept)                                                0.356 0.721766    
## time                                                      21.977  < 2e-16 ***
## ageClass                                                 -27.915  < 2e-16 ***
## factor(reg_name)Bourgogne-Franche-Comté                  -14.139  < 2e-16 ***
## factor(reg_name)Bretagne                                   9.535  < 2e-16 ***
## factor(reg_name)Centre-Val de Loire                        1.461 0.144025    
## factor(reg_name)Corse                                      2.879 0.003987 ** 
## factor(reg_name)Grand Est                                -24.756  < 2e-16 ***
## factor(reg_name)Guadeloupe                                 0.490 0.624305    
## factor(reg_name)Guyane                                    -3.213 0.001315 ** 
## factor(reg_name)Hauts-de-France                           12.700  < 2e-16 ***
## factor(reg_name)Île-de-France                             22.889  < 2e-16 ***
## factor(reg_name)La Réunion                               -15.315  < 2e-16 ***
## factor(reg_name)Martinique                                 2.840 0.004514 ** 
## factor(reg_name)Mayotte                                   -1.402 0.160786    
## factor(reg_name)Normandie                                 -4.544 5.53e-06 ***
## factor(reg_name)Nouvelle-Aquitaine                         2.215 0.026757 *  
## factor(reg_name)Occitanie                                  6.700 2.08e-11 ***
## factor(reg_name)Pays de la Loire                          -9.572  < 2e-16 ***
## factor(reg_name)Provence-Alpes-Côte d'Azur                12.906  < 2e-16 ***
## time:ageClass                                              8.242  < 2e-16 ***
## time:factor(reg_name)Bourgogne-Franche-Comté               2.627 0.008604 ** 
## time:factor(reg_name)Bretagne                              0.355 0.722236    
## time:factor(reg_name)Centre-Val de Loire                  -0.108 0.914152    
## time:factor(reg_name)Corse                                -0.089 0.928897    
## time:factor(reg_name)Grand Est                             5.112 3.19e-07 ***
## time:factor(reg_name)Guadeloupe                            4.547 5.43e-06 ***
## time:factor(reg_name)Guyane                               -1.540 0.123664    
## time:factor(reg_name)Hauts-de-France                       2.884 0.003925 ** 
## time:factor(reg_name)Île-de-France                        -8.420  < 2e-16 ***
## time:factor(reg_name)La Réunion                            1.630 0.103121    
## time:factor(reg_name)Martinique                           -0.785 0.432169    
## time:factor(reg_name)Mayotte                              -0.774 0.439116    
## time:factor(reg_name)Normandie                             6.891 5.53e-12 ***
## time:factor(reg_name)Nouvelle-Aquitaine                    2.697 0.006996 ** 
## time:factor(reg_name)Occitanie                             3.457 0.000547 ***
## time:factor(reg_name)Pays de la Loire                      5.812 6.18e-09 ***
## time:factor(reg_name)Provence-Alpes-Côte d'Azur            4.073 4.64e-05 ***
## ageClass:factor(reg_name)Bourgogne-Franche-Comté           1.948 0.051402 .  
## ageClass:factor(reg_name)Bretagne                          4.537 5.71e-06 ***
## ageClass:factor(reg_name)Centre-Val de Loire               0.778 0.436652    
## ageClass:factor(reg_name)Corse                             5.477 4.34e-08 ***
## ageClass:factor(reg_name)Grand Est                         9.579  < 2e-16 ***
## ageClass:factor(reg_name)Guadeloupe                        2.451 0.014255 *  
## ageClass:factor(reg_name)Guyane                            1.281 0.200064    
## ageClass:factor(reg_name)Hauts-de-France                  11.493  < 2e-16 ***
## ageClass:factor(reg_name)Île-de-France                     4.901 9.54e-07 ***
## ageClass:factor(reg_name)La Réunion                        7.480 7.42e-14 ***
## ageClass:factor(reg_name)Martinique                       -1.620 0.105231    
## ageClass:factor(reg_name)Mayotte                           0.941 0.346479    
## ageClass:factor(reg_name)Normandie                         4.231 2.33e-05 ***
## ageClass:factor(reg_name)Nouvelle-Aquitaine               -3.977 6.97e-05 ***
## ageClass:factor(reg_name)Occitanie                         4.434 9.24e-06 ***
## ageClass:factor(reg_name)Pays de la Loire                 11.213  < 2e-16 ***
## ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur       -1.135 0.256423    
## time:ageClass:factor(reg_name)Bourgogne-Franche-Comté     -0.463 0.643256    
## time:ageClass:factor(reg_name)Bretagne                    -0.544 0.586162    
## time:ageClass:factor(reg_name)Centre-Val de Loire         -0.043 0.965364    
## time:ageClass:factor(reg_name)Corse                       -1.475 0.140337    
## time:ageClass:factor(reg_name)Grand Est                   -4.590 4.44e-06 ***
## time:ageClass:factor(reg_name)Guadeloupe                  -3.403 0.000666 ***
## time:ageClass:factor(reg_name)Guyane                       3.134 0.001723 ** 
## time:ageClass:factor(reg_name)Hauts-de-France             -7.754 8.92e-15 ***
## time:ageClass:factor(reg_name)Île-de-France               -0.092 0.926550    
## time:ageClass:factor(reg_name)La Réunion                  -6.386 1.70e-10 ***
## time:ageClass:factor(reg_name)Martinique                   1.172 0.241101    
## time:ageClass:factor(reg_name)Mayotte                      0.764 0.445095    
## time:ageClass:factor(reg_name)Normandie                   -2.480 0.013120 *  
## time:ageClass:factor(reg_name)Nouvelle-Aquitaine          -1.154 0.248562    
## time:ageClass:factor(reg_name)Occitanie                   -4.621 3.81e-06 ***
## time:ageClass:factor(reg_name)Pays de la Loire            -8.344  < 2e-16 ***
## time:ageClass:factor(reg_name)Provence-Alpes-Côte d'Azur   1.748 0.080522 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   9428.9  on 2978  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 25556
## 
## Number of Fisher Scoring iterations: 8

## Likelihood ratio test
anova(mdl3, mdl0, test="Chisq")

## Analysis of Deviance Table
## 
## Model 1: cbind(V1, notV1) ~ time * ageClass * factor(reg_name)
## Model 2: cbind(V1, notV1) ~ time * factor(ageClass) * factor(reg_name)
##   Resid. Df Resid. Dev  Df Deviance  Pr(>Chi)    
## 1      2978     9428.9                           
## 2      2701     2246.2 277   7182.7 < 2.2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

# GLM
# Assuming that all IND (indetermine) are non-V1
mdl <- glm(cbind(V1, notV1) ~ date2 * as.factor(ageClass) + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl)

## 
## Call:
## glm(formula = cbind(V1, notV1) ~ date2 * as.factor(ageClass) + 
##     reg_name.fac, family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.0968  -0.9147   0.0000   0.9812   7.4498  
## 
## Coefficients:
##                                          Estimate Std. Error z value Pr(>|z|)
## (Intercept)                            -8.002e+02  2.756e+01 -29.034  < 2e-16
## date2                                   4.284e-02  1.475e-03  29.041  < 2e-16
## as.factor(ageClass)14.5                -1.504e+02  3.179e+01  -4.729 2.25e-06
## as.factor(ageClass)24.5                -2.252e+02  3.132e+01  -7.189 6.52e-13
## as.factor(ageClass)34.5                -1.373e+02  3.132e+01  -4.383 1.17e-05
## as.factor(ageClass)44.5                -1.446e+02  3.130e+01  -4.621 3.83e-06
## as.factor(ageClass)54.5                -2.061e+02  3.159e+01  -6.523 6.90e-11
## as.factor(ageClass)64.5                -2.059e+02  3.306e+01  -6.228 4.74e-10
## as.factor(ageClass)74.5                -4.709e+02  3.593e+01 -13.109  < 2e-16
## as.factor(ageClass)84.5                -4.631e+02  3.903e+01 -11.864  < 2e-16
## as.factor(ageClass)94.5                -3.659e+02  4.911e+01  -7.451 9.23e-14
## reg_name.facBourgogne-Franche-Comté    -4.359e-01  9.565e-03 -45.572  < 2e-16
## reg_name.facBretagne                    5.577e-01  1.038e-02  53.740  < 2e-16
## reg_name.facCentre-Val de Loire         9.190e-02  1.016e-02   9.047  < 2e-16
## reg_name.facCorse                       9.734e-01  3.122e-02  31.175  < 2e-16
## reg_name.facGrand Est                  -4.756e-01  7.314e-03 -65.028  < 2e-16
## reg_name.facGuadeloupe                  1.525e+00  6.849e-02  22.261  < 2e-16
## reg_name.facGuyane                     -5.355e-01  1.335e-01  -4.011 6.04e-05
## reg_name.facHauts-de-France             4.959e-01  6.125e-03  80.966  < 2e-16
## reg_name.facÎle-de-France               4.658e-01  5.624e-03  82.834  < 2e-16
## reg_name.facLa Réunion                 -2.754e+00  4.211e-02 -65.413  < 2e-16
## reg_name.facMartinique                  5.186e-01  6.157e-02   8.424  < 2e-16
## reg_name.facMayotte                    -5.023e+00  2.047e-01 -24.534  < 2e-16
## reg_name.facNormandie                   1.275e-01  8.934e-03  14.270  < 2e-16
## reg_name.facNouvelle-Aquitaine          7.811e-03  8.468e-03   0.922  0.35635
## reg_name.facOccitanie                   3.112e-01  7.375e-03  42.199  < 2e-16
## reg_name.facPays de la Loire           -3.283e-02  8.538e-03  -3.845  0.00012
## reg_name.facProvence-Alpes-Côte d'Azur  4.468e-01  6.487e-03  68.876  < 2e-16
## date2:as.factor(ageClass)14.5           8.044e-03  1.702e-03   4.727 2.27e-06
## date2:as.factor(ageClass)24.5           1.205e-02  1.677e-03   7.186 6.69e-13
## date2:as.factor(ageClass)34.5           7.343e-03  1.676e-03   4.381 1.18e-05
## date2:as.factor(ageClass)44.5           7.737e-03  1.675e-03   4.618 3.87e-06
## date2:as.factor(ageClass)54.5           1.102e-02  1.691e-03   6.518 7.13e-11
## date2:as.factor(ageClass)64.5           1.100e-02  1.769e-03   6.220 4.97e-10
## date2:as.factor(ageClass)74.5           2.518e-02  1.923e-03  13.097  < 2e-16
## date2:as.factor(ageClass)84.5           2.475e-02  2.089e-03  11.846  < 2e-16
## date2:as.factor(ageClass)94.5           1.954e-02  2.628e-03   7.433 1.06e-13
##                                           
## (Intercept)                            ***
## date2                                  ***
## as.factor(ageClass)14.5                ***
## as.factor(ageClass)24.5                ***
## as.factor(ageClass)34.5                ***
## as.factor(ageClass)44.5                ***
## as.factor(ageClass)54.5                ***
## as.factor(ageClass)64.5                ***
## as.factor(ageClass)74.5                ***
## as.factor(ageClass)84.5                ***
## as.factor(ageClass)94.5                ***
## reg_name.facBourgogne-Franche-Comté    ***
## reg_name.facBretagne                   ***
## reg_name.facCentre-Val de Loire        ***
## reg_name.facCorse                      ***
## reg_name.facGrand Est                  ***
## reg_name.facGuadeloupe                 ***
## reg_name.facGuyane                     ***
## reg_name.facHauts-de-France            ***
## reg_name.facÎle-de-France              ***
## reg_name.facLa Réunion                 ***
## reg_name.facMartinique                 ***
## reg_name.facMayotte                    ***
## reg_name.facNormandie                  ***
## reg_name.facNouvelle-Aquitaine            
## reg_name.facOccitanie                  ***
## reg_name.facPays de la Loire           ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## date2:as.factor(ageClass)14.5          ***
## date2:as.factor(ageClass)24.5          ***
## date2:as.factor(ageClass)34.5          ***
## date2:as.factor(ageClass)44.5          ***
## date2:as.factor(ageClass)54.5          ***
## date2:as.factor(ageClass)64.5          ***
## date2:as.factor(ageClass)74.5          ***
## date2:as.factor(ageClass)84.5          ***
## date2:as.factor(ageClass)94.5          ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 113412.0  on 3049  degrees of freedom
## Residual deviance:   7502.1  on 3013  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 23559
## 
## Number of Fisher Scoring iterations: 5

# Ignoring IND
mdl.narm <- glm(cbind(V1, notV1.narm) ~ date2 + cl_age90 + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl.narm)

## 
## Call:
## glm(formula = cbind(V1, notV1.narm) ~ date2 + cl_age90 + reg_name.fac, 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##    Min      1Q  Median      3Q     Max  
## -7.787  -1.151   0.000   1.001   8.394  
## 
## Coefficients:
##                                          Estimate Std. Error  z value Pr(>|z|)
## (Intercept)                            -1.133e+03  6.223e+00 -182.136  < 2e-16
## date2                                   6.069e-02  3.331e-04  182.217  < 2e-16
## cl_age90                               -7.529e-03  7.678e-05  -98.052  < 2e-16
## reg_name.facBourgogne-Franche-Comté    -4.902e-01  9.795e-03  -50.044  < 2e-16
## reg_name.facBretagne                    5.748e-01  1.091e-02   52.670  < 2e-16
## reg_name.facCentre-Val de Loire         2.077e-01  1.083e-02   19.180  < 2e-16
## reg_name.facCorse                       1.604e+00  4.178e-02   38.396  < 2e-16
## reg_name.facGrand Est                  -4.678e-01  7.580e-03  -61.714  < 2e-16
## reg_name.facGuadeloupe                  1.515e+00  7.173e-02   21.118  < 2e-16
## reg_name.facGuyane                     -3.838e-01  1.405e-01   -2.732  0.00629
## reg_name.facHauts-de-France             6.132e-01  6.489e-03   94.497  < 2e-16
## reg_name.facÎle-de-France               6.751e-01  5.985e-03  112.801  < 2e-16
## reg_name.facLa Réunion                 -2.693e+00  4.251e-02  -63.359  < 2e-16
## reg_name.facMartinique                  4.591e-01  6.319e-02    7.264 3.75e-13
## reg_name.facMayotte                    -4.962e+00  2.049e-01  -24.220  < 2e-16
## reg_name.facNormandie                   2.165e-01  9.468e-03   22.867  < 2e-16
## reg_name.facNouvelle-Aquitaine          2.485e-03  8.798e-03    0.282  0.77760
## reg_name.facOccitanie                   3.609e-01  7.754e-03   46.546  < 2e-16
## reg_name.facPays de la Loire           -5.727e-02  8.834e-03   -6.483 8.97e-11
## reg_name.facProvence-Alpes-Côte d'Azur  5.567e-01  6.873e-03   80.992  < 2e-16
##                                           
## (Intercept)                            ***
## date2                                  ***
## cl_age90                               ***
## reg_name.facBourgogne-Franche-Comté    ***
## reg_name.facBretagne                   ***
## reg_name.facCentre-Val de Loire        ***
## reg_name.facCorse                      ***
## reg_name.facGrand Est                  ***
## reg_name.facGuadeloupe                 ***
## reg_name.facGuyane                     ** 
## reg_name.facHauts-de-France            ***
## reg_name.facÎle-de-France              ***
## reg_name.facLa Réunion                 ***
## reg_name.facMartinique                 ***
## reg_name.facMayotte                    ***
## reg_name.facNormandie                  ***
## reg_name.facNouvelle-Aquitaine            
## reg_name.facOccitanie                  ***
## reg_name.facPays de la Loire           ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 126975  on 3017  degrees of freedom
## Residual deviance:  10822  on 2998  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 26443
## 
## Number of Fisher Scoring iterations: 5

V2

par(mfrow = c(4, 3))
for(region in tmp){
  subdat <- dat.regions[dat.regions$reg == region, ]
  plot(subdat$date2, subdat$Prc_susp_501Y_V2_3, ylim = c(0, 100), main = regs[as.character(region)], col = colsAge[as.character(subdat$cl_age90)], pch = pchAge[as.character(subdat$cl_age90)], 
       xlab = "date", ylab = "Proportion V2/V3"
       )
}

# Create new colums with information on number of specific PCR tests
# PCR with V2/3 result
dat.regions.ages$V23 <- dat.regions.ages$Nb_susp_501Y_V2_3
# All other PCRs (considering NAs are non-V1)
dat.regions.ages$notV23 <- dat.regions.ages$Nb_tests_PCR_TA_crible - dat.regions.ages$Nb_susp_501Y_V2_3
# All other PCRs with a result (removing NAs)
dat.regions.ages$notV23.narm <- dat.regions.ages$Nb_susp_501Y_V1 + dat.regions.ages$Nb_susp_ABS

# GLM
# Assuming that all IND (indetermine) are non-V23
mdl <- glm(cbind(V23, notV23) ~ date2 + ageClass + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl)

## 
## Call:
## glm(formula = cbind(V23, notV23) ~ date2 + ageClass + reg_name.fac, 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -6.9178  -0.8517  -0.2323   0.4906   5.6835  
## 
## Coefficients:
##                                          Estimate Std. Error z value Pr(>|z|)
## (Intercept)                            -1.306e+02  1.318e+01  -9.909  < 2e-16
## date2                                   6.817e-03  7.052e-04   9.666  < 2e-16
## ageClass                               -2.886e-03  1.637e-04 -17.626  < 2e-16
## reg_name.facBourgogne-Franche-Comté     8.035e-02  2.455e-02   3.273 0.001063
## reg_name.facBretagne                    3.729e-02  2.649e-02   1.408 0.159251
## reg_name.facCentre-Val de Loire        -7.903e-01  3.736e-02 -21.153  < 2e-16
## reg_name.facCorse                      -2.181e+00  2.140e-01 -10.190  < 2e-16
## reg_name.facGrand Est                   1.902e+00  1.415e-02 134.412  < 2e-16
## reg_name.facGuadeloupe                 -1.073e+00  2.254e-01  -4.760 1.94e-06
## reg_name.facGuyane                     -1.373e+01  1.936e+02  -0.071 0.943444
## reg_name.facHauts-de-France            -4.878e-01  1.802e-02 -27.061  < 2e-16
## reg_name.facÎle-de-France               3.912e-01  1.418e-02  27.596  < 2e-16
## reg_name.facLa Réunion                  2.913e+00  2.504e-02 116.350  < 2e-16
## reg_name.facMartinique                 -8.930e-01  2.446e-01  -3.650 0.000262
## reg_name.facMayotte                     3.403e+00  3.476e-02  97.918  < 2e-16
## reg_name.facNormandie                  -1.351e-01  2.504e-02  -5.397 6.77e-08
## reg_name.facNouvelle-Aquitaine         -1.305e-01  2.369e-02  -5.511 3.57e-08
## reg_name.facOccitanie                  -9.857e-01  2.731e-02 -36.095  < 2e-16
## reg_name.facPays de la Loire            5.875e-01  1.922e-02  30.561  < 2e-16
## reg_name.facProvence-Alpes-Côte d'Azur -1.747e-01  1.792e-02  -9.753  < 2e-16
##                                           
## (Intercept)                            ***
## date2                                  ***
## ageClass                               ***
## reg_name.facBourgogne-Franche-Comté    ** 
## reg_name.facBretagne                      
## reg_name.facCentre-Val de Loire        ***
## reg_name.facCorse                      ***
## reg_name.facGrand Est                  ***
## reg_name.facGuadeloupe                 ***
## reg_name.facGuyane                        
## reg_name.facHauts-de-France            ***
## reg_name.facÎle-de-France              ***
## reg_name.facLa Réunion                 ***
## reg_name.facMartinique                 ***
## reg_name.facMayotte                    ***
## reg_name.facNormandie                  ***
## reg_name.facNouvelle-Aquitaine         ***
## reg_name.facOccitanie                  ***
## reg_name.facPays de la Loire           ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 76763.8  on 3049  degrees of freedom
## Residual deviance:  5996.1  on 3030  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 16881
## 
## Number of Fisher Scoring iterations: 15

# Ignoring IND
mdl.narm <- glm(cbind(V23, notV23.narm) ~ date2 + ageClass + reg_name.fac, data = dat.regions.ages, family = "binomial")
summary(mdl.narm)

## 
## Call:
## glm(formula = cbind(V23, notV23.narm) ~ date2 + ageClass + reg_name.fac, 
##     family = "binomial", data = dat.regions.ages)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -7.2702  -0.8302  -0.2305   0.5206   5.6334  
## 
## Coefficients:
##                                          Estimate Std. Error z value Pr(>|z|)
## (Intercept)                            -1.299e+02  1.328e+01  -9.779  < 2e-16
## date2                                   6.782e-03  7.107e-04   9.543  < 2e-16
## ageClass                               -2.845e-03  1.656e-04 -17.181  < 2e-16
## reg_name.facBourgogne-Franche-Comté     6.679e-02  2.457e-02   2.718 0.006565
## reg_name.facBretagne                    2.638e-02  2.652e-02   0.995 0.319943
## reg_name.facCentre-Val de Loire        -7.449e-01  3.740e-02 -19.920  < 2e-16
## reg_name.facCorse                      -2.092e+00  2.141e-01  -9.772  < 2e-16
## reg_name.facGrand Est                   1.948e+00  1.420e-02 137.166  < 2e-16
## reg_name.facGuadeloupe                 -1.125e+00  2.254e-01  -4.991 6.01e-07
## reg_name.facGuyane                     -1.384e+01  2.127e+02  -0.065 0.948116
## reg_name.facHauts-de-France            -4.677e-01  1.805e-02 -25.919  < 2e-16
## reg_name.facÎle-de-France               4.421e-01  1.420e-02  31.129  < 2e-16
## reg_name.facLa Réunion                  3.165e+00  2.643e-02 119.751  < 2e-16
## reg_name.facMartinique                 -9.312e-01  2.447e-01  -3.806 0.000141
## reg_name.facMayotte                     3.561e+00  3.665e-02  97.186  < 2e-16
## reg_name.facNormandie                  -1.015e-01  2.508e-02  -4.049 5.15e-05
## reg_name.facNouvelle-Aquitaine         -1.296e-01  2.371e-02  -5.465 4.63e-08
## reg_name.facOccitanie                  -9.751e-01  2.733e-02 -35.683  < 2e-16
## reg_name.facPays de la Loire            5.833e-01  1.926e-02  30.291  < 2e-16
## reg_name.facProvence-Alpes-Côte d'Azur -1.509e-01  1.794e-02  -8.413  < 2e-16
##                                           
## (Intercept)                            ***
## date2                                  ***
## ageClass                               ***
## reg_name.facBourgogne-Franche-Comté    ** 
## reg_name.facBretagne                      
## reg_name.facCentre-Val de Loire        ***
## reg_name.facCorse                      ***
## reg_name.facGrand Est                  ***
## reg_name.facGuadeloupe                 ***
## reg_name.facGuyane                        
## reg_name.facHauts-de-France            ***
## reg_name.facÎle-de-France              ***
## reg_name.facLa Réunion                 ***
## reg_name.facMartinique                 ***
## reg_name.facMayotte                    ***
## reg_name.facNormandie                  ***
## reg_name.facNouvelle-Aquitaine         ***
## reg_name.facOccitanie                  ***
## reg_name.facPays de la Loire           ***
## reg_name.facProvence-Alpes-Côte d'Azur ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 78608.9  on 3017  degrees of freedom
## Residual deviance:  5898.8  on 2998  degrees of freedom
##   (540 observations deleted due to missingness)
## AIC: 16700
## 
## Number of Fisher Scoring iterations: 15

All

par(mfrow = c(4, 3))
tmp <- unique(dat.regions$reg) # Region codes
tmp <- tmp[tmp>10 & tmp <= 93] # Choose only metropolitan regions
for(region in tmp){
  subdat <- dat.regions[dat.regions$reg == region, ]

  cc <- getVec(subdat[subdat$cl_age90 == 0, ], prop = FALSE)
  plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
  title(main = regs[as.character(region)])
}

Départements

URL <- "https://www.data.gouv.fr/fr/datasets/r/16f4fd03-797f-4616-bca9-78ff212d06e8"
dataFile <- paste0("data/Dep_", today, ".csv") # name file with today's date
download.file(URL, dataFile) # download file from repo
dat.deps <- read.csv(dataFile, sep = ";", stringsAsFactors = FALSE)

# Format date
dat.deps$date1 <- as.Date(substring(dat.deps$semaine, 1, 10))
dat.deps$date2 <- as.Date(substring(dat.deps$semaine, 12, 21))

# Rewrite time as days since beginning of the data
dat.deps$time <- dat.deps$date2 - min(dat.deps$date2)

# Compute data on total tests
dat.deps$Nb_tests_POS <- dat.deps$Nb_tests_PCR_TA_crible / (dat.deps$Prc_tests_PCR_TA_crible / 100)

# Add name
deps <- read.csv("data/departement2020.csv", stringsAsFactors = FALSE)
# Turn into dictionnary
dps <- deps$libelle
names(dps) <- as.character(deps$dep)

dat.deps$departement <- dps[as.character(dat.deps$dep)]

V1

par(mfrow = c(35, 3))
for(idep in sort(unique(dat.deps$dep))){
  tmp <- dat.deps[dat.deps$dep == idep, ]
  plot(tmp$date2, tmp$Prc_susp_501Y_V1, ylim = c(0, 100), col = colsAge[as.character(tmp$cl_age90)], pch = pchAge[as.character(tmp$cl_age90)], 
       xlab = "date", ylab = "Proportion V1", 
       main = unique(tmp$departement))
  
#  legend(x = min(dat.deps$date2), y = 100, legend = ages, pch = pchAge, col = colsAge)
}

V2/V3

par(mfrow = c(35, 3))
for(idep in sort(unique(dat.deps$dep))){
  subdat <- dat.deps[dat.deps$dep == idep, ]
  if(any(!is.na(subdat$Nb_tests_POS))){
    cc <- getVec(subdat[subdat$cl_age90 == 0, ], prop = FALSE)
    plotDist(cc$x, cc$c1, cc$c23, cc$cABS, cc$cIND)
    title(main = unique(subdat$departement))
  }
  
  
#  legend(x = min(dat.deps$date2), y = 100, legend = ages, pch = pchAge, col = colsAge)
}

All